Question: remove in mapping results the reads that aligned > 1 times
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gravatar for cpozacarrion
4 months ago by
cpozacarrion0 wrote:

I would like to remove from the BAM file after mapping using bowtie2 tool, the reads that aligned > 1 times. Any know how remove these reads?. Thanks. César.

alignment bowtie galaxy • 178 views
ADD COMMENTlink modified 4 months ago by Devon Ryan1.6k • written 4 months ago by cpozacarrion0
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gravatar for Devon Ryan
4 months ago by
Devon Ryan1.6k
Germany
Devon Ryan1.6k wrote:

You can use the "Filter SAM or BAM, output SAM or BAM" tool under "NGS: Samtools". Just set the "Minimum MAPQ quality score" (the "quality" is redundant in that label...) to 2. This will remove slightly more than just those alignments that align >1 times, but the difference is minor (if you wanted to truly only remove those alignments counted as "aligned > 1 times" then you'd have to compare the AS and XS auxiliary tags...which is much more of a pain than it's worth)

ADD COMMENTlink written 4 months ago by Devon Ryan1.6k
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