How to extract unique mapped reads from sam alignment file of pair end reads
The mapping was done using bowtie2.
There is different posts for the same topic suggesting to use the 11 , 12 columns AS and XS
Others say Unique alignments in bowtie2 have MAPQ>=2
And which option shall I use for bowtie2 to get an option like -m from bowtie?
3 answers
It depends on how unique unique should be. The only reliable way to select only alignments for which the next best alignment has a lower score is by comparing the AS and XS tags (when they're the same, the MAPQ will be 0 or 1, though the MAPQ can also be 1 if these tags differ). Having said all of that, you're better off filtering at a MAPQ of 5 or so for most purposes.
There is no equivalent of -m in bowtie2 and there's no exact way to implement it in post-processing if you were to use -a.
Yeah, -k isn't really a substitute, since if it has more than what you specify with -k then it'll just won't report some of them, rather than suppressing all of them. Perhaps bowtie2 sets NH appropriately in that case, but I rather doubt it.
•
written
by
Devon Ryan
Actually, you probably could just post-process the output of -a, though that's likely going to be slow.
•
written
by
Devon Ryan
This post basically covers everything: Bowtie2, -M Alignment/Reporting Mode
It includes discussion of the different -k options and the different columns that are added when a read is identified as multiply mapped.
•
written
by
Brice Sarver
+1 Indeed, this is more convenient than comparing AS and XS tags (at least assuming one means "has a second best alignment with an inferior score to the best alignment" by "unique").
Haven't used bowtie2 for a while but if I remember correctly Bowtie2 doesn't generate "NH:" tag for reads in the SAM file. I usually go with concordantly mapped paired-end reads using "YT:Z:CP" tag rather than using MAPQ to extract reliable alignments.
•
written
by
Ashutosh Pandey
no such NH flag Best Way To Get Truly Unique Reads In Bowtie/Sam?
Log in to answer this question.
-
How to extract uniquely mapped reads in Bowtie2
written by Ankit
-
Extract unique and multimapped reads from bowtie 1 sam/bam output
written by Konstantinos Yeles
-
Adding tag XS to HISAT2 sam files perior to StringTie
written by Farbod
-
Speed up Tophat2 running
written by yuabrahamliu •
-
Multiple Hits and Unique Mapped Reads
written by fusion.slope
-
Topcoat error during resuming topcoat pipeline with unmapped reads
written by lingling •
-
TopHat error during aligning reads
written by lingling •
-
Bowtie2 --strata problem
written by Avi Srivastava
-
How to filter unique reads from sam file?
written by Medhat
-
Error while running Tophat 2.0.11
written by subodh •
