I have already had the BAM file, so how can I remove those reads which are not uniquely mapped? Can samtools do this? All some other software?
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I don't like this definition, since suppose a mapper X tries harder to find a hit than mapper Y, then mapper X is most likely more sensitive and specific, but will have fewer reads that only had one hit, even though a hit for a read may be much more likely than all other hits.
That's why you should look at mapping quality. Those with mapping quality zero are ambiguous: multiple equally best alignments were found. But those with higher quality should have higher confidence.
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Originally posted by Heisman View PostLook in the samtools specification... pretty sure there is some type of flag for multiply mapped reads. Then you can convert the file to SAM format and grep -v it.
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If your aligner properly sets the MAPQ field, you can filter on this. After all, if there are two equally plausible alignments, the probability for each alignment to be correct is at most 50%, which transforms to a Phred score of 3. Hence, an aligner should never indicate a mapping quality above 3 for multiply matched reads.
Furthermore, many aligners follow the recommendation to use the optional tag "NH" to indicate how many alignments are reported for this read. This helps only, of course, if you instructed the aligner to report multiple alignments.
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Originally posted by Simon Anders View PostIf your aligner properly sets the MAPQ field, you can filter on this. After all, if there are two equally plausible alignments, the probability for each alignment to be correct is at most 50%, which transforms to a Phred score of 3. Hence, an aligner should never indicate a mapping quality above 3 for multiply matched reads.
Don't want considering only "concordant" reads, since i would like to retain paired reads that map in the same region but with discordant orientation (if stranded)
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