User: Davy
Davy • 360
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Posts by Davy
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... Reads added above. Thanks for the assistance.
...
written 5.4 years ago by
Davy • 360
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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 5.4 years ago by
Davy • 360
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... Thanks, but this gives the same result.
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written 5.4 years ago by
Davy • 360
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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 5.5 years ago by
Davy • 360
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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?
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written 5.5 years ago by
Davy • 360
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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.
...
written 5.5 years ago by
Davy • 360
1
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... Have you tried meme?
http://meme.nbcr.net/meme/
...
written 5.5 years ago by
Davy • 360
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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 5.5 years ago by
Davy • 360
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... As usual, Pierre to the rescue!!!
...
written 5.7 years ago by
Davy • 360
Latest awards to Davy
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For Calculating Gc Content For All Ccds
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For Error In Bioperl Get Adaptor
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For Picard Samtofastq Only Extracts One Read, Then Throws An Error
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For Automated Literature Search For List Of Genes
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For What Are The It Requirements For High Throughput Sequence Analysis
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For Creating Hg19 Reference Index
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For Extracting Read Pairs From Region So That All Pairs Remain Intact
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For C: Why Are There More Non-Synonymous Snps Than Synonymous Snps In The 1000 Genomes
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