DanBest,Hey Shaun,Thanks for the information. I've copied the ABySS Users Google Group on this message, for posterity. Follow up question: how does abyss-map identify reads as uniquely mapped? Is this property indicated in the SAM FLAG column?On Fri, Feb 5, 2016 at 5:19 PM, Shaun Jackman <sjac...@gmail.com> wrote:Hi, Dan. I don’t believe the MAPQ values of
abyss-map
are documented anywhere. Sorry for that. ABySS does not calculate a proper MAPQ value. To do that it would need to keep track of the second-best hit, and it doesn’t do that. The MAPQ value ofabyss-map
is the same as the alignment score, which is the number of matched nucleotides, or 0 in the case of a multimap. TheMAPQ
value is capped at 254.I’m happy to answer e-mail questions, but if you send your question instead to BioStars, GitHub or Google Groups, the question and answer will be publicly archived for future Googlers.
- https://www.biostars.org/t/abyss/
- https://github.com/bcgsc/abyss/issues
- https://groups.google.com/forum/#!forum/abyss-users
Cheers,
Shaun
On 2016-February-05 at 13:08:10 , Dan Browne (dbrow...@gmail.com) wrote:
Hi Shaun,I've been experimenting with abyss-map recently, capturing the standard SAM output as follows (ABySS version 1.9.0):
abyss-map -v -j20 -l125 ../../02_Separated_Pairs/Library.SXPX.L.fq.gz ../../02_Separated_Pairs/Library.SXPX.R.fq.gz ../../SXPX_SEQ1K_99-3.fa | abyss-fixmate --all --qname -v | samtools view -@20 -Sb - | samtools sort -@ 20 -O bam -T MAP_SXPX_SEQ1K_99_OLC > MAP_SXPX_SEQ1K_99_OLC.bam && samtools index MAP_SXPX_SEQ1K_99_OLC.bamSee the attached file for the inspection of the SAM file and the resulting MAPQs. I've never seen such high MAPQ values, and I am just wondering how abyss-map calculates the MAPQ? Am I missing something trivial?
I look forward to your insight.
Best,Dan
Oh wait, I just re-read your email and think I figured it out. Anything with a score of 0 is a multimap, so basically anything with an alignment score above the minimum threshold (-l) is mapped uniquely?Dan
On Sun, Feb 7, 2016 at 12:52 PM, Dan Browne wrote:
DanBest,Hey Shaun,Thanks for the information. I've copied the ABySS Users Google Group on this message, for posterity. Follow up question: how does abyss-map identify reads as uniquely mapped? Is this property indicated in the SAM FLAG column?
On Fri, Feb 5, 2016 at 5:19 PM, Shaun Jackman wrote:
Hi, Dan. I don’t believe the MAPQ values of
abyss-map
are documented anywhere. Sorry for that. ABySS does not calculate a proper MAPQ value. To do that it would need to keep track of the second-best hit, and it doesn’t do that. The MAPQ value ofabyss-map
is the same as the alignment score, which is the number of matched nucleotides, or 0 in the case of a multimap. TheMAPQ
value is capped at 254.I’m happy to answer e-mail questions, but if you send your question instead to BioStars, GitHub or Google Groups, the question and answer will be publicly archived for future Googlers.
- https://www.biostars.org/t/abyss/
- https://github.com/bcgsc/abyss/issues
- https://groups.google.com/forum/#!forum/abyss-users
Cheers,
Shaun