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I want to ask about the difference between outSAMstrandField intronMotif and outFilterIntronMotifs RemoveNoncanonical.
According to the info. from the STAR --help,
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.
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.
The text was updated successfully, but these errors were encountered:
Dear community,
I want to ask about the difference between
outSAMstrandField intronMotif
andoutFilterIntronMotifs RemoveNoncanonical
.According to the info. from the STAR --help,
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.outFilterIntronMotifs RemoveNoncanonical
: filter out alignments that contain non-canonical junctionsAre 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.
The text was updated successfully, but these errors were encountered: