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Old 03-27-2019, 05:20 AM   #1
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Location: France

Join Date: Apr 2014
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Default StringTie merge- can someone help me understand its output?


I am currently using StringTie merge on a StringTie output in order to discover genes that are not already in my reference annotation. I tried looking at the documentation but it is not very clear to me how to distinguish some things in the output or how it proceeds.

The command I have been using is :
${stringtie} --merge -G reference.gtf -o genome.StringTie.merged.gtf -F 1 -l GenomeX GenomeX.StringTie.sorted.gtf
with GenomeX.StringTie.sorted.gtf the output of stringTie.

I do not exactly understand how it works: when it finds a region which maps or overlaps, does it replace the line from "GenomeX..." by the line from "reference.gtf"?
Also, what is the difference with this command?

${stringtie} --merge -o genome.StringTie.merged.gtf -F 1 -l GenomeX listGenomes.gtf
with listGenomes.gtf being:

When I looked at the output of the second command, I did not see how we can distinguish between "reference.gtf" lines and "GenomeX.StringTie.sorted.gtf", or which field I am supposed to look at. Is there a way to do so after a merge?Also, does it choose between the two files when a region is similar?

Thanks a lot for reading me,

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