Hello,
we are using RNA-Star to our project (thank to authors!).
I don't understand a difference observed about the SJ.out.tab files (file with junctions) according to the value of 'outFilterType' option (Normal or BySJout).
Indeed, Alexander Dobin wrote (https://groups.google.com/forum/#!ms...w/VmgoGKSE9qQJ) :
"However, if you use --outFilterType BySJout option, splicing of alignments in the Aligned.out.sam will only be allowed across the junctions which pass the filtering into SJ.out.tab.
This option makes Aligment.out.sam file consistent with SJ.out.tab file."
So I had understood that the SJ.out.tab files should be the same, but not the sam files (file with alignments, from which the SJ.out.tab is created).
But I have two different SJ.out.tab files (all options except outFilterType are identical).
Could anyone explain to me why?
The other options are:
--outSJfilterReads unique --outSJfilterOverhangMin 29 12 12 12 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05 --outFilterIntronMotifs None --alignSJoverhangMin 5
Thanks!
we are using RNA-Star to our project (thank to authors!).
I don't understand a difference observed about the SJ.out.tab files (file with junctions) according to the value of 'outFilterType' option (Normal or BySJout).
Indeed, Alexander Dobin wrote (https://groups.google.com/forum/#!ms...w/VmgoGKSE9qQJ) :
"However, if you use --outFilterType BySJout option, splicing of alignments in the Aligned.out.sam will only be allowed across the junctions which pass the filtering into SJ.out.tab.
This option makes Aligment.out.sam file consistent with SJ.out.tab file."
So I had understood that the SJ.out.tab files should be the same, but not the sam files (file with alignments, from which the SJ.out.tab is created).
But I have two different SJ.out.tab files (all options except outFilterType are identical).
Could anyone explain to me why?
The other options are:
--outSJfilterReads unique --outSJfilterOverhangMin 29 12 12 12 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05 --outFilterIntronMotifs None --alignSJoverhangMin 5
Thanks!
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