part of gene structure is white

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part of gene structure is white

mictadlo
Hello,
I ran StringTie and converted its results to GFF3 with the following commands:

> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3

I dragged the StringTie annotation and dropped it into the yellow annotation field and some part of the gene remained white and some changed the colour.

Screen Shot 2019-10-03 at 3.58.10 PM.png

Why only half of the gene colour changed and not all?

Thank you in advance,

Michal 

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Re: part of gene structure is white

Michael Paulini

Hi Michal,

I would guess that the coloured bits are the longest ORF (with a different colour for each exon frame) and the white bits UTR.

Michael

On 03/10/2019 07:25, Michał T. Lorenc wrote:
Hello,
I ran StringTie and converted its results to GFF3 with the following commands:

> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3

I dragged the StringTie annotation and dropped it into the yellow annotation field and some part of the gene remained white and some changed the colour.

Screen Shot 2019-10-03 at 3.58.10 PM.png

Why only half of the gene colour changed and not all?

Thank you in advance,

Michal 
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Re: part of gene structure is white

nathandunn

This is correct.  The CDS are colored directly.  If you right-click and view the GFF3 to confirm this.   


Nathan


On Oct 3, 2019, at 1:34 AM, Michael Paulini <[hidden email]> wrote:

Hi Michal,

I would guess that the coloured bits are the longest ORF (with a different colour for each exon frame) and the white bits UTR.

Michael

On 03/10/2019 07:25, Michał T. Lorenc wrote:
Hello,
I ran StringTie and converted its results to GFF3 with the following commands:

> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3

I dragged the StringTie annotation and dropped it into the yellow annotation field and some part of the gene remained white and some changed the colour.

<Screen Shot 2019-10-03 at 3.58.10 PM.png>

Why only half of the gene colour changed and not all?

Thank you in advance,

Michal 
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Re: part of gene structure is white

mictadlo
Hi Nathan and Michael,
The following GFF3 I have got from "Get GFF3":

##gff-version 3
##sequence-region NbV1Ch12 1 179405951
NbV1Ch12 . gene 38409881 38418096 . - . owner=xx;ID=f57b0047-89d8-4bf9-a56e-64394054e653;date_last_modified=2019-10-03;Name=MSTRG.19428.1;date_creation=2019-10-03
NbV1Ch12 . mRNA 38409987 38418096 . - . owner=[hidden email];Parent=f57b0047-89d8-4bf9-a56e-64394054e653;ID=4e698d8d-9e82-466b-a08f-a2db25249f06;date_last_modified=2019-10-03;Name=MSTRG.19428.1-00002;date_creation=2019-10-03
NbV1Ch12 . exon 38417819 38418096 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=89299921-f3cb-475a-91e6-dcc0cfb452cd;Name=89299921-f3cb-475a-91e6-dcc0cfb452cd
NbV1Ch12 . exon 38413645 38414564 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=0199ae59-2978-4760-984d-ab93739eb8eb;Name=0199ae59-2978-4760-984d-ab93739eb8eb
NbV1Ch12 . exon 38412622 38413584 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=f2e50d82-2db8-4aff-b1ff-9b65831bce1b;Name=f2e50d82-2db8-4aff-b1ff-9b65831bce1b
NbV1Ch12 . exon 38409987 38410939 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=9f4d537c-1505-4f1d-b91e-bf056bc0604e;Name=9f4d537c-1505-4f1d-b91e-bf056bc0604e
NbV1Ch12 . CDS 38415788 38416294 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38413645 38414564 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38412622 38413584 . - 1 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38411065 38411215 . - 1 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38410118 38410939 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . exon 38411065 38411215 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=412af113-aadd-44b2-9508-00b25337631e;Name=412af113-aadd-44b2-9508-00b25337631e
NbV1Ch12 . exon 38415788 38416350 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=ea34304d-da91-4ec7-b13d-92dbe6e5a8d0;Name=ea34304d-da91-4ec7-b13d-92dbe6e5a8d0
###

This is BAM track:
Screen Shot 2019-10-09 at 11.31.39 AM.png

Thank you in advance,

Best wishes,

Michal

On Fri, Oct 4, 2019 at 12:46 AM Nathan Dunn <[hidden email]> wrote:

This is correct.  The CDS are colored directly.  If you right-click and view the GFF3 to confirm this.   


Nathan


On Oct 3, 2019, at 1:34 AM, Michael Paulini <[hidden email]> wrote:

Hi Michal,

I would guess that the coloured bits are the longest ORF (with a different colour for each exon frame) and the white bits UTR.

Michael

On 03/10/2019 07:25, Michał T. Lorenc wrote:
Hello,
I ran StringTie and converted its results to GFF3 with the following commands:

> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3

I dragged the StringTie annotation and dropped it into the yellow annotation field and some part of the gene remained white and some changed the colour.

<Screen Shot 2019-10-03 at 3.58.10 PM.png>

Why only half of the gene colour changed and not all?

Thank you in advance,

Michal 
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Re: part of gene structure is white

Jacques Dainat-4
Hello,

From what we see in the first image, the gene model from the user track should have 3 CDS parts, but what you get from "Get GFF3” shows 5 CDS parts… strange.
I experienced similar issue in the past (weird drawing of the gene model), and it was due to errors in the gff3 file I loaded. But when you get it from Webapollo by  "Get GFF3” it is somehow reformatted in something coherent. You should extract the locus using awk in the original gff3 file to check how it is in the originally (and show us the result).
awk '{if ($1=="NbV1Ch12" && $4 > 38409000 && $5 < 38419000) print $0}’ file.gff

Best regards,

Jacques
-------------------------------------------------
Jacques Dainat, Ph.D.
NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
http://nbis.se/about/staff/jacques-dainat


On 9 Oct 2019, at 03:44, Michał T. Lorenc <[hidden email]> wrote:

Hi Nathan and Michael,
The following GFF3 I have got from "Get GFF3":

##gff-version 3
##sequence-region NbV1Ch12 1 179405951
NbV1Ch12 . gene 38409881 38418096 . - . owner=xx;ID=f57b0047-89d8-4bf9-a56e-64394054e653;date_last_modified=2019-10-03;Name=MSTRG.19428.1;date_creation=2019-10-03
NbV1Ch12 . mRNA 38409987 38418096 . - . owner=[hidden email];Parent=f57b0047-89d8-4bf9-a56e-64394054e653;ID=4e698d8d-9e82-466b-a08f-a2db25249f06;date_last_modified=2019-10-03;Name=MSTRG.19428.1-00002;date_creation=2019-10-03
NbV1Ch12 . exon 38417819 38418096 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=89299921-f3cb-475a-91e6-dcc0cfb452cd;Name=89299921-f3cb-475a-91e6-dcc0cfb452cd
NbV1Ch12 . exon 38413645 38414564 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=0199ae59-2978-4760-984d-ab93739eb8eb;Name=0199ae59-2978-4760-984d-ab93739eb8eb
NbV1Ch12 . exon 38412622 38413584 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=f2e50d82-2db8-4aff-b1ff-9b65831bce1b;Name=f2e50d82-2db8-4aff-b1ff-9b65831bce1b
NbV1Ch12 . exon 38409987 38410939 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=9f4d537c-1505-4f1d-b91e-bf056bc0604e;Name=9f4d537c-1505-4f1d-b91e-bf056bc0604e
NbV1Ch12 . CDS 38415788 38416294 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38413645 38414564 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38412622 38413584 . - 1 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38411065 38411215 . - 1 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38410118 38410939 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . exon 38411065 38411215 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=412af113-aadd-44b2-9508-00b25337631e;Name=412af113-aadd-44b2-9508-00b25337631e
NbV1Ch12 . exon 38415788 38416350 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=ea34304d-da91-4ec7-b13d-92dbe6e5a8d0;Name=ea34304d-da91-4ec7-b13d-92dbe6e5a8d0
###

This is BAM track:
<Screen Shot 2019-10-09 at 11.31.39 AM.png>

Thank you in advance,

Best wishes,

Michal

On Fri, Oct 4, 2019 at 12:46 AM Nathan Dunn <[hidden email]> wrote:

This is correct.  The CDS are colored directly.  If you right-click and view the GFF3 to confirm this.   

<PastedGraphic-1.png>

Nathan


On Oct 3, 2019, at 1:34 AM, Michael Paulini <[hidden email]> wrote:

Hi Michal,

I would guess that the coloured bits are the longest ORF (with a different colour for each exon frame) and the white bits UTR.

Michael

On 03/10/2019 07:25, Michał T. Lorenc wrote:
Hello,
I ran StringTie and converted its results to GFF3 with the following commands:

> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3

I dragged the StringTie annotation and dropped it into the yellow annotation field and some part of the gene remained white and some changed the colour.

<Screen Shot 2019-10-03 at 3.58.10 PM.png>

Why only half of the gene colour changed and not all?

Thank you in advance,

Michal 
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Re: part of gene structure is white

mictadlo
Hi Jacques,
Thank you for your reply. I did everything from scratch:

$ awk '{if ($1=="NbV1Ch12" && $4 > 38409000 && $5 < 38419000) print $0}' stringtie_merged.gff3
NbV1Ch12 StringTie mRNA 38409881 38418003 1000.00 - . ID=MSTRG.19428.1;geneID=MSTRG.19428
NbV1Ch12 StringTie exon 38409881 38410939 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie exon 38411065 38411215 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie exon 38412622 38414564 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie exon 38415788 38416350 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie exon 38417583 38418003 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie mRNA 38409952 38418003 1000.00 - . ID=MSTRG.19428.2;geneID=MSTRG.19428
NbV1Ch12 StringTie exon 38409952 38411215 1000.00 - . Parent=MSTRG.19428.2
NbV1Ch12 StringTie exon 38412622 38414564 1000.00 - . Parent=MSTRG.19428.2
NbV1Ch12 StringTie exon 38415788 38416350 1000.00 - . Parent=MSTRG.19428.2
NbV1Ch12 StringTie exon 38417819 38418003 1000.00 - . Parent=MSTRG.19428.2
NbV1Ch12 StringTie mRNA 38409952 38418003 1000.00 - . ID=MSTRG.19428.3;geneID=MSTRG.19428
NbV1Ch12 StringTie exon 38409952 38410939 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie exon 38411065 38411215 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie exon 38412622 38414564 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie exon 38415788 38416350 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie exon 38417819 38418003 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie mRNA 38410031 38417981 1000.00 - . ID=MSTRG.19428.4;geneID=MSTRG.19428
NbV1Ch12 StringTie exon 38410031 38410939 1000.00 - . Parent=MSTRG.19428.4
NbV1Ch12 StringTie exon 38412622 38414564 1000.00 - . Parent=MSTRG.19428.4
NbV1Ch12 StringTie exon 38415788 38416350 1000.00 - . Parent=MSTRG.19428.4
NbV1Ch12 StringTie exon 38417819 38417981 1000.00 - . Parent=MSTRG.19428.4

'Get GFF3' gave me this:
##gff-version 3
##sequence-region NbV1Ch12 1 179405951
NbV1Ch12 . gene 38409952 38418003 . - . owner=xx;ID=d4197433-fbae-45a3-83da-638738cb9b71;date_last_modified=2019-10-10;Name=MSTRG.19428.2;date_creation=2019-10-10
NbV1Ch12 . mRNA 38409952 38418003 . - . owner=xx;Parent=d4197433-fbae-45a3-83da-638738cb9b71;ID=5d80cb40-9109-4129-ac8c-ad61221d94dd;date_last_modified=2019-10-10;Name=MSTRG.19428.2-00001;date_creation=2019-10-10
NbV1Ch12 . exon 38415788 38416350 . - . Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=3aacc2b6-a573-4724-9c8f-a6848d42c104;Name=3aacc2b6-a573-4724-9c8f-a6848d42c104
NbV1Ch12 . exon 38412622 38414564 . - . Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=462f3697-c4ad-4ad7-afe3-cbc2436eaceb;Name=462f3697-c4ad-4ad7-afe3-cbc2436eaceb
NbV1Ch12 . CDS 38415788 38416294 . - 0 Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=5d80cb40-9109-4129-ac8c-ad61221d94dd-CDS;Name=5d80cb40-9109-4129-ac8c-ad61221d94dd-CDS
NbV1Ch12 . CDS 38413632 38414564 . - 0 Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=5d80cb40-9109-4129-ac8c-ad61221d94dd-CDS;Name=5d80cb40-9109-4129-ac8c-ad61221d94dd-CDS
NbV1Ch12 . exon 38409952 38411215 . - . Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=16b5aadb-b8e5-43e5-93a9-b2a6cc2ffdeb;Name=16b5aadb-b8e5-43e5-93a9-b2a6cc2ffdeb
NbV1Ch12 . exon 38417819 38418003 . - . Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=be9c18f4-c796-4446-b3c3-49088de492b1;Name=be9c18f4-c796-4446-b3c3-49088de492b1
###

Screen Shot 2019-10-10 at 8.37.38 PM.png

I do not understand why there are the 3 white blocks?

Thank you in advance,

Michal


On Wed, Oct 9, 2019 at 6:30 PM Jacques Dainat <[hidden email]> wrote:
Hello,

From what we see in the first image, the gene model from the user track should have 3 CDS parts, but what you get from "Get GFF3” shows 5 CDS parts… strange.
I experienced similar issue in the past (weird drawing of the gene model), and it was due to errors in the gff3 file I loaded. But when you get it from Webapollo by  "Get GFF3” it is somehow reformatted in something coherent. You should extract the locus using awk in the original gff3 file to check how it is in the originally (and show us the result).
awk '{if ($1=="NbV1Ch12" && $4 > 38409000 && $5 < 38419000) print $0}’ file.gff

Best regards,

Jacques
-------------------------------------------------
Jacques Dainat, Ph.D.
NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
http://nbis.se/about/staff/jacques-dainat


On 9 Oct 2019, at 03:44, Michał T. Lorenc <[hidden email]> wrote:

Hi Nathan and Michael,
The following GFF3 I have got from "Get GFF3":

##gff-version 3
##sequence-region NbV1Ch12 1 179405951
NbV1Ch12 . gene 38409881 38418096 . - . owner=xx;ID=f57b0047-89d8-4bf9-a56e-64394054e653;date_last_modified=2019-10-03;Name=MSTRG.19428.1;date_creation=2019-10-03
NbV1Ch12 . mRNA 38409987 38418096 . - . owner=[hidden email];Parent=f57b0047-89d8-4bf9-a56e-64394054e653;ID=4e698d8d-9e82-466b-a08f-a2db25249f06;date_last_modified=2019-10-03;Name=MSTRG.19428.1-00002;date_creation=2019-10-03
NbV1Ch12 . exon 38417819 38418096 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=89299921-f3cb-475a-91e6-dcc0cfb452cd;Name=89299921-f3cb-475a-91e6-dcc0cfb452cd
NbV1Ch12 . exon 38413645 38414564 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=0199ae59-2978-4760-984d-ab93739eb8eb;Name=0199ae59-2978-4760-984d-ab93739eb8eb
NbV1Ch12 . exon 38412622 38413584 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=f2e50d82-2db8-4aff-b1ff-9b65831bce1b;Name=f2e50d82-2db8-4aff-b1ff-9b65831bce1b
NbV1Ch12 . exon 38409987 38410939 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=9f4d537c-1505-4f1d-b91e-bf056bc0604e;Name=9f4d537c-1505-4f1d-b91e-bf056bc0604e
NbV1Ch12 . CDS 38415788 38416294 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38413645 38414564 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38412622 38413584 . - 1 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38411065 38411215 . - 1 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38410118 38410939 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . exon 38411065 38411215 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=412af113-aadd-44b2-9508-00b25337631e;Name=412af113-aadd-44b2-9508-00b25337631e
NbV1Ch12 . exon 38415788 38416350 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=ea34304d-da91-4ec7-b13d-92dbe6e5a8d0;Name=ea34304d-da91-4ec7-b13d-92dbe6e5a8d0
###

This is BAM track:
<Screen Shot 2019-10-09 at 11.31.39 AM.png>

Thank you in advance,

Best wishes,

Michal

On Fri, Oct 4, 2019 at 12:46 AM Nathan Dunn <[hidden email]> wrote:

This is correct.  The CDS are colored directly.  If you right-click and view the GFF3 to confirm this.   

<PastedGraphic-1.png>

Nathan


On Oct 3, 2019, at 1:34 AM, Michael Paulini <[hidden email]> wrote:

Hi Michal,

I would guess that the coloured bits are the longest ORF (with a different colour for each exon frame) and the white bits UTR.

Michael

On 03/10/2019 07:25, Michał T. Lorenc wrote:
Hello,
I ran StringTie and converted its results to GFF3 with the following commands:

> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3

I dragged the StringTie annotation and dropped it into the yellow annotation field and some part of the gene remained white and some changed the colour.

<Screen Shot 2019-10-03 at 3.58.10 PM.png>

Why only half of the gene colour changed and not all?

Thank you in advance,

Michal 
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Screen Shot 2019-10-10 at 8.37.38 PM.png (74K) Download Attachment
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Re: part of gene structure is white

Jacques Dainat-4
Hi,

This makes more sense now.
Your off file is from Stringtie, so it is not an annotation in the sense we don’t know what is coding or not. So it contains only exon features. The exons colour is white (you can change that if you wish). When you load the mRNA into the user-track, Webapollo determines automatically the longest ORF and will create the corresponding CDS features (It also creates the gene feature to which it attaches the mRNA feature). The CDS are coloured depending the frame. So everything is normal. The remaining parts are still exon and stay white.
If you wish an annotation, which will contains CDS and UTRs you need to provide your Stringtie transcriptome to an annotation tool like MAKER. 

/Jacques

On 10 Oct 2019, at 13:05, Michał T. Lorenc <[hidden email]> wrote:

Hi Jacques,
Thank you for your reply. I did everything from scratch:

$ awk '{if ($1=="NbV1Ch12" && $4 > 38409000 && $5 < 38419000) print $0}' stringtie_merged.gff3
NbV1Ch12 StringTie mRNA 38409881 38418003 1000.00 - . ID=MSTRG.19428.1;geneID=MSTRG.19428
NbV1Ch12 StringTie exon 38409881 38410939 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie exon 38411065 38411215 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie exon 38412622 38414564 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie exon 38415788 38416350 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie exon 38417583 38418003 1000.00 - . Parent=MSTRG.19428.1
NbV1Ch12 StringTie mRNA 38409952 38418003 1000.00 - . ID=MSTRG.19428.2;geneID=MSTRG.19428
NbV1Ch12 StringTie exon 38409952 38411215 1000.00 - . Parent=MSTRG.19428.2
NbV1Ch12 StringTie exon 38412622 38414564 1000.00 - . Parent=MSTRG.19428.2
NbV1Ch12 StringTie exon 38415788 38416350 1000.00 - . Parent=MSTRG.19428.2
NbV1Ch12 StringTie exon 38417819 38418003 1000.00 - . Parent=MSTRG.19428.2
NbV1Ch12 StringTie mRNA 38409952 38418003 1000.00 - . ID=MSTRG.19428.3;geneID=MSTRG.19428
NbV1Ch12 StringTie exon 38409952 38410939 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie exon 38411065 38411215 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie exon 38412622 38414564 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie exon 38415788 38416350 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie exon 38417819 38418003 1000.00 - . Parent=MSTRG.19428.3
NbV1Ch12 StringTie mRNA 38410031 38417981 1000.00 - . ID=MSTRG.19428.4;geneID=MSTRG.19428
NbV1Ch12 StringTie exon 38410031 38410939 1000.00 - . Parent=MSTRG.19428.4
NbV1Ch12 StringTie exon 38412622 38414564 1000.00 - . Parent=MSTRG.19428.4
NbV1Ch12 StringTie exon 38415788 38416350 1000.00 - . Parent=MSTRG.19428.4
NbV1Ch12 StringTie exon 38417819 38417981 1000.00 - . Parent=MSTRG.19428.4

'Get GFF3' gave me this:
##gff-version 3
##sequence-region NbV1Ch12 1 179405951
NbV1Ch12 . gene 38409952 38418003 . - . owner=xx;ID=d4197433-fbae-45a3-83da-638738cb9b71;date_last_modified=2019-10-10;Name=MSTRG.19428.2;date_creation=2019-10-10
NbV1Ch12 . mRNA 38409952 38418003 . - . owner=xx;Parent=d4197433-fbae-45a3-83da-638738cb9b71;ID=5d80cb40-9109-4129-ac8c-ad61221d94dd;date_last_modified=2019-10-10;Name=MSTRG.19428.2-00001;date_creation=2019-10-10
NbV1Ch12 . exon 38415788 38416350 . - . Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=3aacc2b6-a573-4724-9c8f-a6848d42c104;Name=3aacc2b6-a573-4724-9c8f-a6848d42c104
NbV1Ch12 . exon 38412622 38414564 . - . Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=462f3697-c4ad-4ad7-afe3-cbc2436eaceb;Name=462f3697-c4ad-4ad7-afe3-cbc2436eaceb
NbV1Ch12 . CDS 38415788 38416294 . - 0 Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=5d80cb40-9109-4129-ac8c-ad61221d94dd-CDS;Name=5d80cb40-9109-4129-ac8c-ad61221d94dd-CDS
NbV1Ch12 . CDS 38413632 38414564 . - 0 Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=5d80cb40-9109-4129-ac8c-ad61221d94dd-CDS;Name=5d80cb40-9109-4129-ac8c-ad61221d94dd-CDS
NbV1Ch12 . exon 38409952 38411215 . - . Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=16b5aadb-b8e5-43e5-93a9-b2a6cc2ffdeb;Name=16b5aadb-b8e5-43e5-93a9-b2a6cc2ffdeb
NbV1Ch12 . exon 38417819 38418003 . - . Parent=5d80cb40-9109-4129-ac8c-ad61221d94dd;ID=be9c18f4-c796-4446-b3c3-49088de492b1;Name=be9c18f4-c796-4446-b3c3-49088de492b1
###

<Screen Shot 2019-10-10 at 8.37.38 PM.png>

I do not understand why there are the 3 white blocks?

Thank you in advance,

Michal


On Wed, Oct 9, 2019 at 6:30 PM Jacques Dainat <[hidden email]> wrote:
Hello,

From what we see in the first image, the gene model from the user track should have 3 CDS parts, but what you get from "Get GFF3” shows 5 CDS parts… strange.
I experienced similar issue in the past (weird drawing of the gene model), and it was due to errors in the gff3 file I loaded. But when you get it from Webapollo by  "Get GFF3” it is somehow reformatted in something coherent. You should extract the locus using awk in the original gff3 file to check how it is in the originally (and show us the result).
awk '{if ($1=="NbV1Ch12" && $4 > 38409000 && $5 < 38419000) print $0}’ file.gff

Best regards,

Jacques
-------------------------------------------------
Jacques Dainat, Ph.D.
NBIS (National Bioinformatics Infrastructure Sweden)
Genome Annotation Service
http://nbis.se/about/staff/jacques-dainat


On 9 Oct 2019, at 03:44, Michał T. Lorenc <[hidden email]> wrote:

Hi Nathan and Michael,
The following GFF3 I have got from "Get GFF3":

##gff-version 3
##sequence-region NbV1Ch12 1 179405951
NbV1Ch12 . gene 38409881 38418096 . - . owner=xx;ID=f57b0047-89d8-4bf9-a56e-64394054e653;date_last_modified=2019-10-03;Name=MSTRG.19428.1;date_creation=2019-10-03
NbV1Ch12 . mRNA 38409987 38418096 . - . owner=[hidden email];Parent=f57b0047-89d8-4bf9-a56e-64394054e653;ID=4e698d8d-9e82-466b-a08f-a2db25249f06;date_last_modified=2019-10-03;Name=MSTRG.19428.1-00002;date_creation=2019-10-03
NbV1Ch12 . exon 38417819 38418096 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=89299921-f3cb-475a-91e6-dcc0cfb452cd;Name=89299921-f3cb-475a-91e6-dcc0cfb452cd
NbV1Ch12 . exon 38413645 38414564 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=0199ae59-2978-4760-984d-ab93739eb8eb;Name=0199ae59-2978-4760-984d-ab93739eb8eb
NbV1Ch12 . exon 38412622 38413584 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=f2e50d82-2db8-4aff-b1ff-9b65831bce1b;Name=f2e50d82-2db8-4aff-b1ff-9b65831bce1b
NbV1Ch12 . exon 38409987 38410939 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=9f4d537c-1505-4f1d-b91e-bf056bc0604e;Name=9f4d537c-1505-4f1d-b91e-bf056bc0604e
NbV1Ch12 . CDS 38415788 38416294 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38413645 38414564 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38412622 38413584 . - 1 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38411065 38411215 . - 1 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . CDS 38410118 38410939 . - 0 Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=b975d482-a37c-4258-b9be-e3eebb1762ba;Name=b975d482-a37c-4258-b9be-e3eebb1762ba
NbV1Ch12 . exon 38411065 38411215 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=412af113-aadd-44b2-9508-00b25337631e;Name=412af113-aadd-44b2-9508-00b25337631e
NbV1Ch12 . exon 38415788 38416350 . - . Parent=4e698d8d-9e82-466b-a08f-a2db25249f06;ID=ea34304d-da91-4ec7-b13d-92dbe6e5a8d0;Name=ea34304d-da91-4ec7-b13d-92dbe6e5a8d0
###

This is BAM track:
<Screen Shot 2019-10-09 at 11.31.39 AM.png>

Thank you in advance,

Best wishes,

Michal

On Fri, Oct 4, 2019 at 12:46 AM Nathan Dunn <[hidden email]> wrote:

This is correct.  The CDS are colored directly.  If you right-click and view the GFF3 to confirm this.   

<PastedGraphic-1.png>

Nathan


On Oct 3, 2019, at 1:34 AM, Michael Paulini <[hidden email]> wrote:

Hi Michal,

I would guess that the coloured bits are the longest ORF (with a different colour for each exon frame) and the white bits UTR.

Michael

On 03/10/2019 07:25, Michał T. Lorenc wrote:
Hello,
I ran StringTie and converted its results to GFF3 with the following commands:

> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3

I dragged the StringTie annotation and dropped it into the yellow annotation field and some part of the gene remained white and some changed the colour.

<Screen Shot 2019-10-03 at 3.58.10 PM.png>

Why only half of the gene colour changed and not all?

Thank you in advance,

Michal 
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<Screen Shot 2019-10-10 at 8.37.38 PM.png>

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