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alexdobin / STAR

RNA-seq aligner
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What's the difference between "outSAMstrandField" and "outFilterIntronMotifs RemoveNoncanonical" #2237

Open hungweichen0327 opened 2 weeks ago

hungweichen0327 commented 2 weeks ago

Dear community,

I want to ask about the difference between outSAMstrandField intronMotif and outFilterIntronMotifs RemoveNoncanonical. According to the info. from the STAR --help,

  1. outSAMstrandField intronMotif: strand derived from the intron motif. This option changes the output alignments: reads with inconsistent and/or non-canonical introns are filtered out.
  2. outFilterIntronMotifs RemoveNoncanonical: filter out alignments that contain non-canonical junctions

Are they the same? But it seems that outSAMstrandField intronMotif not only filter alignments that contain non-canonical junctions but also alignments that contain inconsistent junctions.

Thank you.