What's the difference about SJ.out.tab files?

[kyoungmin Lee]

Hey everybody!!

I have a question.

After the alignment, there are many SJ.out.tab files.

e.g. there are many SRR prefix SJ.out.tab such as SRR12345678__SJ.out.tab 

but there is a just SJ.out.tab file without any prefix SRR.

It seems like value of 7th, 8th and 9th columns are different which are "#of uniquely mapping reads spanning the splice junction" , "# of multimapping reads spanning the splice junction" and "maximum spliced alignement overhang". 

[Alexander Dobin]

Hi,

it seems multiple jobs were run from the same directory.

The SRR12345678__SJ.out.tab files was generated by a job which used --outFileNamePrefix  SRR12345678__

SJ.out.tab was generated by a job without --outFileNamePrefix option.

Cheers

Alex