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julienrichardalbert / MEA

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Using --outFilterType BySJout for STAR #8

Closed michael-kotliar closed 6 years ago

michael-kotliar commented 6 years ago

Can I omit this parameter when running STAR alignReads? --outFilterType BySJout If I understood correctly from STAR manual, we need it to

keep only those reads that contain junctions that passed filtering into SJ.out.tab

and

By default --outSJfilter* parameters do not affect alignments in the Aligned.out.sam file. 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

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But when we created STAR indices we didn't use any annotation file, so there is no data about spliced junctions?

julienrichardalbert commented 6 years ago

This logic is correct. In addition to not using any annotation file, we do not specify outSJfilter* options, so --outSJfilterType BySJout probably does nothing in this context. I will empirically test this today and remove this parameter from mea.config if the results hold true. Cheers!