User: rbronste
rbronste • 120
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Posts by rbronste
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... Yes will take a look at the memory issue, did not run out of disk space however. This is indeed from a high output NextSeq run. Just one PE run. ...
written 3 days ago by
rbronste • 120
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... Yes you are correct after checking the log:
Using the latest version of clumpify as I just downloaded BBMap, memory allocation being an issue is weird since it was running on cluster node. The node job was dumped but I missed that fact, many temp files accumulated actually. Cutadapt was run separat ...
written 3 days ago by
rbronste • 120
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... I would think tools along the lines of DAVID, GOrrilla or GSEA could put you on your way to finding out general functional categories. They are good tools in well established systems such as cancer biology and hematopoiesis but not as good in areas such as neuroscience, the terms can be somewhat ge ...
written 4 days ago by
rbronste • 120
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... Thanks for the breakdown, I am doing ATAC-seq so trying to understand the overall pros/cons in that application. ...
written 4 days ago by
rbronste • 120
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... How are the files changed following this process (example command below), tried after to run them through cutadapt (output below) to remove adapter sequences and got the following:
bash clumpify.sh in1= in2= out1= out2= dedupe optical dupedist=40 spany=t
unexpected end of file
cutadap ...
written 4 days ago by
rbronste • 120
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... What would be optimal command for removing only optical duplicates specifically from PE reads? Thanks. ...
written 4 days ago by
rbronste • 120
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... Wondering about pros/cons of removing duplicates from the raw fastq files vs the raw BAM alignment? Thanks. ...
written 4 days ago by
rbronste • 120
• updated
4 days ago by
Istvan Albert ♦♦ 73k
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Comment:
C: Samtools flagstat unpaired reads
... Yes just for BAM files already processed for removal of duplicates (Picard) and ChrM and ChrUN reads. ...
written 4 days ago by
rbronste • 120
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... Trying to quickly remove reads samtools flagstat deems as unpaired from BAM file? Thanks. ...
written 4 days ago by
rbronste • 120
• updated
4 days ago by
Pierre Lindenbaum ♦ 96k
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... Wondering about opinions on duplicate removal for such things as foot printing in ATAC data. It seems as though Picard at least is extremely aggressive in this regard and removes large amounts of duplicates vs samtools rmdup in my experience. Though Macs2 peaks called with small number of remaining ...
written 5 days ago by
rbronste • 120
• updated
4 days ago by
James Ashmore • 1.7k
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