[Gmod-ajax] About bam file in JBrowse

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[Gmod-ajax] About bam file in JBrowse

Sansheng Chen
Hi! All,

I just upload bam file to JBrowse, then I found most of the reads have same length, however, some of them are extremely larger than others. 

Show in this picture:
In the right side, these reads are longer than left side.
Inline image 1

Besides, from sam file, the reads information show some of the reads are not match with reference sequence very well, so, I wonder know if in JBrowse, the long read just cover the unmatched part? Thanks!

Inline image 2

sincerely, 
sansheng


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Re: About bam file in JBrowse

Ke Jiang
Can you check the cigar string for those reads? if you see some 'D' there, which means there are deletions in these reads, this may make sense. 

Ke

On Wednesday, September 9, 2015, Sansheng Chen <[hidden email]> wrote:
Hi! All,

I just upload bam file to JBrowse, then I found most of the reads have same length, however, some of them are extremely larger than others. 

Show in this picture:
In the right side, these reads are longer than left side.
Inline image 1

Besides, from sam file, the reads information show some of the reads are not match with reference sequence very well, so, I wonder know if in JBrowse, the long read just cover the unmatched part? Thanks!

Inline image 2

sincerely, 
sansheng


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Re: About bam file in JBrowse

Ke Jiang
In reply to this post by Sansheng Chen
Oh, I see, those are caused by the Ns in your reference assembly. 

Ke

On Wednesday, September 9, 2015, Sansheng Chen <[hidden email]> wrote:
Hi! All,

I just upload bam file to JBrowse, then I found most of the reads have same length, however, some of them are extremely larger than others. 

Show in this picture:
In the right side, these reads are longer than left side.
Inline image 1

Besides, from sam file, the reads information show some of the reads are not match with reference sequence very well, so, I wonder know if in JBrowse, the long read just cover the unmatched part? Thanks!

Inline image 2

sincerely, 
sansheng


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Re: About bam file in JBrowse

Keiran Raine
Hi Sansheng,

N in the cigar indicates a skipped region of the reference not alignment to N in the reference, although it can be the case (it's not here as you have short alignments within the skip region based on the image).

It looks like you aren't using the Alignments2 features, I'd recommend seeing how they render before anything else.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 9 Sep 2015, at 22:11, Ke Jiang <[hidden email]> wrote:

Oh, I see, those are caused by the Ns in your reference assembly. 

Ke

On Wednesday, September 9, 2015, Sansheng Chen <[hidden email]> wrote:
Hi! All,

I just upload bam file to JBrowse, then I found most of the reads have same length, however, some of them are extremely larger than others. 

Show in this picture:
In the right side, these reads are longer than left side.
<Screen Shot 2015-09-09 at 2.17.27 PM.png>

Besides, from sam file, the reads information show some of the reads are not match with reference sequence very well, so, I wonder know if in JBrowse, the long read just cover the unmatched part? Thanks!

<Screen Shot 2015-09-09 at 2.21.39 PM.png>

sincerely, 
sansheng

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Re: About bam file in JBrowse

Sansheng Chen
Hi, Keiran,

What is alignments 2 feature? Is this is a function when I running tophat? Because I just got this bam file from tophat directly, then I upload the bam file into JBrowse. I know that this column just represent reads matched information, however, even there many medium region can't be matched with reference, the reads length should be the same, like they all got from RNA-seq data. But, in JBrowse, some reads are very long.
If you know why there exist long reads, please let me know. Thank you very much!

sincerely,
sansheng

On Thu, Sep 10, 2015 at 3:28 AM, Keiran Raine <[hidden email]> wrote:
Hi Sansheng,

N in the cigar indicates a skipped region of the reference not alignment to N in the reference, although it can be the case (it's not here as you have short alignments within the skip region based on the image).

It looks like you aren't using the Alignments2 features, I'd recommend seeing how they render before anything else.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 9 Sep 2015, at 22:11, Ke Jiang <[hidden email]> wrote:

Oh, I see, those are caused by the Ns in your reference assembly. 

Ke

On Wednesday, September 9, 2015, Sansheng Chen <[hidden email]> wrote:
Hi! All,

I just upload bam file to JBrowse, then I found most of the reads have same length, however, some of them are extremely larger than others. 

Show in this picture:
In the right side, these reads are longer than left side.
<Screen Shot 2015-09-09 at 2.17.27 PM.png>

Besides, from sam file, the reads information show some of the reads are not match with reference sequence very well, so, I wonder know if in JBrowse, the long read just cover the unmatched part? Thanks!

<Screen Shot 2015-09-09 at 2.21.39 PM.png>

sincerely, 
sansheng

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Re: About bam file in JBrowse

Keiran Raine
Hi Sansheng,

'Alignments2' refers to the type of rendering applied to your track in JBrowse and is not related to how the aligner works:


What you are seeing is likely to be a read that spans an exon boundary, the 'N' elements being the point the split mapping spans, alignments2 should give you something more like this (I've checked the red spanning read and cigar is 42M2676N33M):



Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 10 Sep 2015, at 14:50, Sansheng Chen <[hidden email]> wrote:

Hi, Keiran,

What is alignments 2 feature? Is this is a function when I running tophat? Because I just got this bam file from tophat directly, then I upload the bam file into JBrowse. I know that this column just represent reads matched information, however, even there many medium region can't be matched with reference, the reads length should be the same, like they all got from RNA-seq data. But, in JBrowse, some reads are very long.
If you know why there exist long reads, please let me know. Thank you very much!

sincerely,
sansheng

On Thu, Sep 10, 2015 at 3:28 AM, Keiran Raine <[hidden email]> wrote:
Hi Sansheng,

N in the cigar indicates a skipped region of the reference not alignment to N in the reference, although it can be the case (it's not here as you have short alignments within the skip region based on the image).

It looks like you aren't using the Alignments2 features, I'd recommend seeing how they render before anything else.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 9 Sep 2015, at 22:11, Ke Jiang <[hidden email]> wrote:

Oh, I see, those are caused by the Ns in your reference assembly. 

Ke

On Wednesday, September 9, 2015, Sansheng Chen <[hidden email]> wrote:
Hi! All,

I just upload bam file to JBrowse, then I found most of the reads have same length, however, some of them are extremely larger than others. 

Show in this picture:
In the right side, these reads are longer than left side.
<Screen Shot 2015-09-09 at 2.17.27 PM.png>

Besides, from sam file, the reads information show some of the reads are not match with reference sequence very well, so, I wonder know if in JBrowse, the long read just cover the unmatched part? Thanks!

<Screen Shot 2015-09-09 at 2.21.39 PM.png>

sincerely, 
sansheng

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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: About bam file in JBrowse

Keiran Raine
Hi,

You need to discuss this with the administrator of your JBrowse instance.  If it is your own install please use the list to get support from the team

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 10 Sep 2015, at 15:42, Sansheng Chen <[hidden email]> wrote:

Hi! Keiran,

Thank you! I'll try to use this configuration. But, umm, I don't know how to add this options. Could you please show an example about the track configuration? Like how to change the HideDuplicateReads, I want to show the duplicate. Where can I change the default setting? Thanks!

<Screen Shot 2015-09-10 at 10.39.19 AM.png>

On Thu, Sep 10, 2015 at 10:09 AM, Keiran Raine <[hidden email]> wrote:
Hi Sansheng,

'Alignments2' refers to the type of rendering applied to your track in JBrowse and is not related to how the aligner works:


What you are seeing is likely to be a read that spans an exon boundary, the 'N' elements being the point the split mapping spans, alignments2 should give you something more like this (I've checked the red spanning read and cigar is 42M2676N33M):

<Screen Shot 2015-09-10 at 15.07.38.png>

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 10 Sep 2015, at 14:50, Sansheng Chen <[hidden email]> wrote:

Hi, Keiran,

What is alignments 2 feature? Is this is a function when I running tophat? Because I just got this bam file from tophat directly, then I upload the bam file into JBrowse. I know that this column just represent reads matched information, however, even there many medium region can't be matched with reference, the reads length should be the same, like they all got from RNA-seq data. But, in JBrowse, some reads are very long.
If you know why there exist long reads, please let me know. Thank you very much!

sincerely,
sansheng

On Thu, Sep 10, 2015 at 3:28 AM, Keiran Raine <[hidden email]> wrote:
Hi Sansheng,

N in the cigar indicates a skipped region of the reference not alignment to N in the reference, although it can be the case (it's not here as you have short alignments within the skip region based on the image).

It looks like you aren't using the Alignments2 features, I'd recommend seeing how they render before anything else.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 9 Sep 2015, at 22:11, Ke Jiang <[hidden email]> wrote:

Oh, I see, those are caused by the Ns in your reference assembly. 

Ke

On Wednesday, September 9, 2015, Sansheng Chen <[hidden email]> wrote:
Hi! All,

I just upload bam file to JBrowse, then I found most of the reads have same length, however, some of them are extremely larger than others. 

Show in this picture:
In the right side, these reads are longer than left side.
<Screen Shot 2015-09-09 at 2.17.27 PM.png>

Besides, from sam file, the reads information show some of the reads are not match with reference sequence very well, so, I wonder know if in JBrowse, the long read just cover the unmatched part? Thanks!

<Screen Shot 2015-09-09 at 2.21.39 PM.png>

sincerely, 
sansheng

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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: About bam file in JBrowse

Ke Jiang
In reply to this post by Sansheng Chen
Hi, Sansheng,

Alignments2 is a JBrowse track type for BAM files. You use this to tweak the appearance of read alignment on JBrowse. For example, you'll see the following text in your 'tracks.conf' file a track using 'Alignments2' (notice the red text), which will probably show the big gap in the reads that span exon/intron junctions.

Cheers.

Ke

# mRNA expression
[tracks . mRNA_BAM ]
label = mRNA read alignments
key = mRNA read alignments
category =   mRNA / BAM
storeClass = JBrowse/Store/SeqFeature/BAM
urlTemplate=  ../../raw/XXXXXXXXX/sample_1.bam
type = JBrowse/View/Track/Alignments2


On Thu, Sep 10, 2015 at 9:50 AM, Sansheng Chen <[hidden email]> wrote:
Hi, Keiran,

What is alignments 2 feature? Is this is a function when I running tophat? Because I just got this bam file from tophat directly, then I upload the bam file into JBrowse. I know that this column just represent reads matched information, however, even there many medium region can't be matched with reference, the reads length should be the same, like they all got from RNA-seq data. But, in JBrowse, some reads are very long.
If you know why there exist long reads, please let me know. Thank you very much!

sincerely,
sansheng

On Thu, Sep 10, 2015 at 3:28 AM, Keiran Raine <[hidden email]> wrote:
Hi Sansheng,

N in the cigar indicates a skipped region of the reference not alignment to N in the reference, although it can be the case (it's not here as you have short alignments within the skip region based on the image).

It looks like you aren't using the Alignments2 features, I'd recommend seeing how they render before anything else.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%C2%A0Ext%3A%207703" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 7703
Office: H104

On 9 Sep 2015, at 22:11, Ke Jiang <[hidden email]> wrote:

Oh, I see, those are caused by the Ns in your reference assembly. 

Ke

On Wednesday, September 9, 2015, Sansheng Chen <[hidden email]> wrote:
Hi! All,

I just upload bam file to JBrowse, then I found most of the reads have same length, however, some of them are extremely larger than others. 

Show in this picture:
In the right side, these reads are longer than left side.
<Screen Shot 2015-09-09 at 2.17.27 PM.png>

Besides, from sam file, the reads information show some of the reads are not match with reference sequence very well, so, I wonder know if in JBrowse, the long read just cover the unmatched part? Thanks!

<Screen Shot 2015-09-09 at 2.21.39 PM.png>

sincerely, 
sansheng

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