Re: Extract all features between two genome positions

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Re: Extract all features between two genome positions

nathandunn

Alexis.  I think you have to become a member of the group to post to the list:  https://groups.google.com/a/lbl.gov/

Please let me know if I should update instructions anywhere for that (or if you need any other help).

Adding the issue is fine as well: https://github.com/GMOD/Apollo/issues/2214





Trying to determine what type of result you are looking for, for this problem.   A few scenarios:

1 - The GFF3 of all features in the region from each track (based on whatever the JBrowse reports (similar to what JBrowse does now for each track).




2 - Interpreted FASTA (what we do in the annotation area):




Nathan

On Jul 24, 2019, at 8:14 AM, Alexis GROPPI <[hidden email]> wrote:

Hi,

We have an instance of Apollo 2.2.0 running in our lab. I have several tracks (BlastP, BlastX, Pfam, RNA prediction, ...)

Is there an way to extract all the features between 2 genome positions ?

For example as in the screenshot here attached :

- genome positions : chr1:7859996..7869996

Features :

Trinity_FM14_mRNA_Assembly : TRINITY_GG_5284_c4_g1_i1.p1

Braker2_mRNA_Prediction : jg27497.t1.p1

BlastX_prediction_hits_Plant : jg27497.t1.p1.SPL6_ORYSJ.1

BlastP_prediction_hits_Plant : jg27497.t1.p1.SPL12_ARATH.1

REPET_TEs_Elements : PF03110.SBP.SBP_domain

Thanks

Alexis Groppi

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