Question: Any tool to output unmapped or mapped_with_clips reads from a BAM to two fastq files for PE data?
2
gravatar for chen
19 months ago by
chen1.8k
OpenGene
chen1.8k wrote:

Hi,

I am processing pair-end sequencing data. I want to output the reads that are unmapped to reference genome or mapped with soft/hard clips, to two fastq files (say R1.fq, R2.fq).

Is there any existing tool available to do this? If not, I will have to develop it by myself.

fastq bam unmapped • 771 views
ADD COMMENTlink modified 19 months ago by Pierre Lindenbaum118k • written 19 months ago by chen1.8k
0
gravatar for Devon Ryan
19 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Unmapped reads can be found with samtools view -f 4. If you need those with soft/hard clipping then use pysam and parse the cigartuples item.

ADD COMMENTlink written 19 months ago by Devon Ryan89k

But this only output the single reads, not the pair.

For pair-end data, if any read of a pair is unmapped or mapped with clips, I'd like to output both reads of this pair.

ADD REPLYlink written 19 months ago by chen1.8k

Use -f 5 then. It will give you unmapped but paired reads. You can play around with the flags, using this tool.

ADD REPLYlink written 19 months ago by ATpoint15k

You'll need to do two passes, where you make a hash of the read names in the first pass and then output them in the second. You can do that in python with pysam, C with htslib, or java with htsjdk. I would suggest using python, it'll be quicker to write.

ADD REPLYlink written 19 months ago by Devon Ryan89k
0
gravatar for Pierre Lindenbaum
19 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

select unmappeds read or clipped reads with , say samjdk http://lindenb.github.io/jvarkit/SamJdk.html (many other solutions are available, search biostars.org)

java -jar dist/samjdk.jar -o out.bam -e 'return record.getReadUnmappedFlag() || record.getCigar().getCigarElements().stream().anyMatch(C->C.getOperator().isClipping());'  in.bam

then use picard SamToFastq to convert back to fastq

http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq

ADD COMMENTlink modified 19 months ago • written 19 months ago by Pierre Lindenbaum118k

I'd like to output both reads of this pair.

more complicated: You need to get the names of the reads after filtering (with samtools view + cut) , and then use http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads + READ_LIST_FILE to get the read with the same names.

ADD REPLYlink written 19 months ago by Pierre Lindenbaum118k
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