User: Davy
Davy • 370
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Posts by Davy
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... Reads added above. Thanks for the assistance.
...
written 6.9 years ago by
Davy • 370
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... So I tried FixMateInformation, and that didn't work. I also tried (emphasis on tried) filtering with samtools view -f (tried 2 and 3 here) but I didn't really get anywhere. Samtools flagstat reports 0 singletons but picard now says "Found 2587 unpaired mates". Any other suggestions, let me know, bu ...
written 6.9 years ago by
Davy • 370
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... Thanks, but this gives the same result.
...
written 6.9 years ago by
Davy • 370
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8 follow
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... Hi all,
I have some whole exome data and I am only interested in the exons of 4 genes, which I have in a bed file.
I ,perhap naively, tried extracting only those reads using this bed file with samtools
samtools view -b -L 4genes.bed myBAM.bam > myBAM.4genes.bam
which works fine, except when I ...
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... Thanks Fabio and Arno. I will continue to seek opinions, but this does make sense to me, so I will continue on with the pipeline for now. Cheers!
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written 7.0 years ago by
Davy • 370
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... Can you explain why I wouldn't need to remove the duplicates? If there is an error early on in the PCR cycle won't that propagate and cause spurious SNP detection, in addition to artificially inflating the read depth?
...
written 7.0 years ago by
Davy • 370
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... I used the standard bwa aln in version 0.6.2. The fastQC reports showed the tails of the reads to quite low quality, so I will try BWA-mem to see if the alignment quality improves.
Cheers. ...
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... Have you tried meme?
http://meme.nbcr.net/meme/
...
written 7.0 years ago by
Davy • 370
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... Hi All,
Recently I have been given some targeted iontorrent sequencing data to play with. It's not large amount of data only ~ 18,000 unpaired reads.
I have aligned the reads with BWA, pretty much the same as I have always done with illumina fastq files. (about 80% aligned, which seemed a bit low, b ...
written 7.0 years ago by
Davy • 370
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... As usual, Pierre to the rescue!!!
...
written 7.2 years ago by
Davy • 370
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