User: hohoku

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hohoku0
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Posts by hohoku

<prev • 9 results • page 1 of 1 • next >
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Answer: A: How would you filter PCR duplicates for merged paired-end reads
... I found that the software [Paleomix][1] has the exact tool I was looking for. `paleomix rmdup_collapsed --remove-duplicates < sorted.bam > < out.bam >` [1]: https://paleomix.readthedocs.io/en/latest/other_tools.html#paleomix-rmdup-collapsed ...
written 4 weeks ago by hohoku0
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Comment: C: How would you filter PCR duplicates for merged paired-end reads
... Yes, same library... I'm not that bad ...
written 5 weeks ago by hohoku0
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Comment: C: How would you filter PCR duplicates for merged paired-end reads
... Yes, I am aware of clumpify and do like it, but sometimes when we sequence more of our sample at a later date, often substantially more, it is more practical to just merge bam files of all the lanes of sequencing than go back to the fastqs, merge them all, deduplicate and map again. ...
written 5 weeks ago by hohoku0
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Comment: C: How would you filter PCR duplicates for merged paired-end reads
... I see your point, but I'm still interested in how to solve this problem. It only requires identifying alignments with identical 5' and 3' ends, so I thought someone here might know a neat way to do it. ...
written 5 weeks ago by hohoku0
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How would you filter PCR duplicates for merged paired-end reads
... I have some paired-end sequencing data that has a significant number of pairs that overlap due to small insert sizes. In my experience, merging the read pairs (and recalibrating with bbmap) results in better alignments. However, when it comes to the PCR duplicate removal step of the merged read pair ...
alignment bam pcr duplicate written 5 weeks ago by hohoku0
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Comment: C: How do I filter a BAM file for proper pairs WITHOUT samtools
... I would normally agree, but we have reasons for not using samtools in this instance ...
written 9 weeks ago by hohoku0
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Answer: A: How do I filter a BAM file for proper pairs WITHOUT samtools
... Thanks for the above responses, but we also found Sambamba which is pretty fast `sambamba view -f bam -F "proper_pair" -o output.bam input.bam` ...
written 9 weeks ago by hohoku0
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Comment: C: How do I filter a BAM file for proper pairs WITHOUT samtools
... We have some conflicts with samtools ...
written 9 weeks ago by hohoku0
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How do I filter a BAM file for proper pairs WITHOUT samtools
... I need to remove unpaired reads from my BAM file... and I'm looking for a non-samtools way of doing it. Suggestions? ...
alignment written 9 weeks ago by hohoku0

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Scholar 4 weeks ago, created an answer that has been accepted. For A: How would you filter PCR duplicates for merged paired-end reads

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