Question: Creating a gtf annotation file from a FASTA (& bam?) for non-model organism
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gravatar for sdbaney
3 months ago by
sdbaney0
sdbaney0 wrote:

I performed de novo transcriptome assembly. Have the FASTA file that I am using as my reference and also performed alignments of my reads back to that. I have been using stringtie to create gtf files for the differential expression analysis (counting requires a gtf file) but I am trying to do this at gene level. Stringtie creates its own IDs for alternative splicing/isoforms. I do not want this. I can't see a way around this so is there a way I can create a gtf annotation file based on my fasta file I use for my reference?

rna-seq • 161 views
ADD COMMENTlink written 3 months ago by sdbaney0

Try SuperTranscripts (can be constructed by Lace or utility in Trinity).

ADD REPLYlink modified 3 months ago • written 3 months ago by SMK1.8k

![enter image description here][1]So I ran supertranscripts (which I am using that FASTA file from it) but the gtf file it gave with it, gave really really odd entries. Here is a snapshot of it:

supertranscripts.gtf

https://ibb.co/NC9HF89

ADD REPLYlink modified 3 months ago • written 3 months ago by sdbaney0

First, let's fix the picture: How to add images to a Biostars :-)

ADD REPLYlink modified 3 months ago • written 3 months ago by SMK1.8k

supertranscripts

Did this work?

ADD REPLYlink written 3 months ago by sdbaney0

Screen-Shot-2019-05-27-at-8-29-22-PM

or this....

ADD REPLYlink written 3 months ago by sdbaney0
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