Open adthrasher opened 8 months ago
Hello, and apologies if this duplicates another issue. I searched but didn't see anything.
When running bowtie in a mode to output multiple alignments, I was surprised to see that additional alignments were not given the secondary alignment flag.
bowtie
secondary alignment
When running the following command
bowtie --chunkmbs=256 -l 51 -p 1 -k 2 -m 2 -X 600 --fr -S bowtie_index/GRCh37.p13.genome.fa-index -1 test.r1.fq -2 test.r2.fq
I get the expected 2 alignments. However, I was expecting the second pair of alignment records to have the secondary flag.
A00637:141:HFYKGDRXX:2:2269:27389:25661 99 chr1 953546 255 51M = 953784 289 GGTGCTGATTGGTGTATTTACAATCCCTGAGCTAGACATAAAGGTTCTCCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF XA:i:0 MD:Z:51 NM:i:0 XM:i:2 A00637:141:HFYKGDRXX:2:2269:27389:25661 147 chr1 953784 255 51M = 953546 -289 GGAGGGGGTGGGAGGCTCAGGCATGGTGGGCTGCAGGTCCCCAGCTCTTCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF XA:i:1 MD:Z:48G2 NM:i:1 XM:i:2 A00637:141:HFYKGDRXX:2:2269:27389:25661 99 chr1 953423 255 51M = 953784 412 GGTGCTGATTGGTGTATTTACAATCCCTGAGCTAGACATAAAGGTTCTCCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF XA:i:2 MD:Z:0A4C45 NM:i:2 XM:i:2 A00637:141:HFYKGDRXX:2:2269:27389:25661 147 chr1 953784 255 51M = 953423 -412 GGAGGGGGTGGGAGGCTCAGGCATGGTGGGCTGCAGGTCCCCAGCTCTTCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF XA:i:1 MD:Z:48G2 NM:i:1 XM:i:2
Is there an option to enable flagging that I have missed? Thanks!
Hello, and apologies if this duplicates another issue. I searched but didn't see anything.
When running
bowtie
in a mode to output multiple alignments, I was surprised to see that additional alignments were not given thesecondary alignment
flag.When running the following command
I get the expected 2 alignments. However, I was expecting the second pair of alignment records to have the secondary flag.
Is there an option to enable flagging that I have missed? Thanks!