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

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kyoungmin Lee

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May 4, 2022, 5:53:03 PMMay 4
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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

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May 13, 2022, 2:36:44 PMMay 13
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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
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