Question: picard.jar SamToFastq "paired reads have different names"
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gravatar for sami.hailu.15
4.1 years ago by
sami.hailu.150 wrote:

Hi,

I'm trying to convert a bam file into paired fastq files using picard:

picard.jar SamToFastq input.bam F=one.fq F2=two.fq NON_PF=true

But the oputput files one.fq and two.fq seem to have different names for paired reads. Can someone suggest me other ways of generating paired reads with same name?

Thanks Sami

sequencing alignment picard • 1.5k views
ADD COMMENTlink modified 4.1 years ago by genomax89k • written 4.1 years ago by sami.hailu.150

See @Brian's answer here for an alternate option: How to extract all the mapped reads from bwa output

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by genomax89k
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