Question: Filter hits that aligned concordantly exactly 1 times base on mpq>40
0
gravatar for User000
3.3 years ago by
User000380
User000380 wrote:

Hello,

I need to get all reads that aligned concordantly exactly 1 times base on mpq>40 from hisat2.

samtools view -b -q 40 -o output.bam alignments.bam

Will this command make a job?

samtools bam • 1.0k views
ADD COMMENTlink modified 3.3 years ago by Brian Bushnell17k • written 3.3 years ago by User000380
2
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

I assume "make a job" means "work". Yes, that will work.

ADD COMMENTlink written 3.3 years ago by Devon Ryan95k
1

Provided samtools was added before view in the command posted :)

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax85k

yes, sorry, I deleted it accidentally before posting! thanks guys

ADD REPLYlink written 3.3 years ago by User000380
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