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Hello,
I am unsure of how to interpret XM:i:1 in SAM as produced by Bowtie. In Bowtie manual (http://bowtie-bio.sourceforge.net/ma...-bowtie-output) it says:
"XM:i:<N> For a read with no reported alignments, <N> is 0 if the read had no alignments. If -m was specified and the read's alignments were supressed because the -m ceiling was exceeded, <N> equals the -m ceiling + 1, to indicate that there were at least that many valid alignments (but all were suppressed)."
I am running bowtie with -m 1. I assume that with this option I suppress reporting the alignments for reads that are aligned more than once. It seems to me, from the description above, that reads suppressed due to -m 1 should have <N> equal to 3 (ceiling '2' plus '1'). However, I can only see XM:i:0 or XM:i:1 in the output file.
Can anybody please explain me the logic of the XM:i:<N> field? Thanks very much.
I am unsure of how to interpret XM:i:1 in SAM as produced by Bowtie. In Bowtie manual (http://bowtie-bio.sourceforge.net/ma...-bowtie-output) it says:
"XM:i:<N> For a read with no reported alignments, <N> is 0 if the read had no alignments. If -m was specified and the read's alignments were supressed because the -m ceiling was exceeded, <N> equals the -m ceiling + 1, to indicate that there were at least that many valid alignments (but all were suppressed)."
I am running bowtie with -m 1. I assume that with this option I suppress reporting the alignments for reads that are aligned more than once. It seems to me, from the description above, that reads suppressed due to -m 1 should have <N> equal to 3 (ceiling '2' plus '1'). However, I can only see XM:i:0 or XM:i:1 in the output file.
Can anybody please explain me the logic of the XM:i:<N> field? Thanks very much.
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