Question: gene IDs in stringtie output
0
gravatar for blooming.daisy333
9 months ago by
blooming.daisy33350 wrote:

Dear All,

Im using stringTie to assemble the transcripts using my genome annotation file with -G flag. but stringTie assigns its own IDs like MSTRG .1, MSTRG.2 to genes and MSTRG1.1 and MSTRG 2,1 to transcripts despite of using geneom annotation file and im unable to get same gene IDs as to that in genome annotation file. I need those IDs for subsequent functional analysis. Can anyone suggest me how to get the same IDs in stringtie output as to that in genome annotation file????

thanks in anticipation

rna-seq • 685 views
ADD COMMENTlink modified 6 months ago by arshad129240 • written 9 months ago by blooming.daisy33350

Hello blooming.daisy333,

Don't forget to follow up on your threads. Please give some feedback to the answers/comments on your last questions:

fin swimmer

ADD REPLYlink written 9 months ago by finswimmer11k

Dear finswimmer, I really appreciate your kind and quick help and im extremely sorry for the delay but im still working on those questions. actually these are interconnected for my analysis. I wiill surely give you the comments like have given before. please give me some time. further for some posts that solved my problem, i could not see any upvote/accepted sign to click on. thats why they are not marked.

ADD REPLYlink written 9 months ago by blooming.daisy33350

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

Please do the same for your previous posts as well.

ADD REPLYlink written 9 months ago by genomax64k

one way is to intersect each mstrg coordinates with known transcriptome gtf @ blooming.daisy333

ADD REPLYlink written 7 months ago by cpad011211k

Hello, I am having the same issue as I am getting MSTG ID instead of gene name. Were you able to solve this issue? If yes, please help me and let me know how did you do it?

Many thanks

ADD REPLYlink written 6 months ago by arshad129240

Please don't ask question in the space reserved for answers, use the ADD COMMENT button instead.

ADD REPLYlink written 6 months ago by h.mon24k

Sorry about that. I am new and didn't realize this.

ADD REPLYlink written 5 months ago by arshad129240
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