Closed eboyden closed 8 months ago
Hello,
I pushed a change to the bug_fixes
that should resolve this issue. Please confirm whether the change does in-fact resolve the issue, so that I can have a release out ASAP.
/bowtie2/bowtie2-bug_fixes/bowtie2 -p 16 --very-sensitive --no-discordant --no-mixed --sam-append-comment -x /bowtie2/index/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set_masked_t14 --interleaved fastq.gz
10374067 reads; of these:
10374067 (100.00%) were paired; of these:
175112 (1.69%) aligned concordantly 0 times
9700465 (93.51%) aligned concordantly exactly 1 time
498490 (4.81%) aligned concordantly >1 times
98.31% overall alignment rate
Looks fixed to me. The total aligned and unaligned read counts are the same, and the mean target coverage is exactly identical to that using 2.4.5, but I did notice that the number of "unique" and the number of "non-unique" alignments reported are slightly different. I assume this is intended, as described in the 2.5.0 release notes: Changed the way that unique alignments are counted in summary message to better match up with filters on SAM output
?
Thanks @ch4rr0, as always I appreciate how responsive you are and how well supported this software is!
Thank you for the kind words.
I assume this is intended, as described in the 2.5.0 release notes: Changed the way that unique alignments are counted in summary message to better match up with filters on SAM output?
That is correct.
When running an identical command on the same input, the alignment rate is substantially lower with 2.5.0 than with 2.4.5: