Moderator: Philipp Bayer
Philipp Bayer ♦ 4.6k
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org
Posts by Philipp Bayer
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Answer:
A: extracting data from bam file
... You could use bedtools genomecov aka genomeCoverageBed, slightly adjusted from the [manual][1]:
samtools view -b chr3:123545-123965 | genomeCoverageBed -ibam stdin
Add -bga to genomeCoverageBed if you want a different format which will also report bases with 0 coverage.
[1]: http://bedtoo ...
written 13 days ago by
Philipp Bayer ♦ 4.6k
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Answer:
A: SRA record can not be found!
... Looks like that submission was started but never finished: https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=SRA112617
I've done that myself before, registered the accession so I had something for the paper, and then completely forgot about it. There's a chance the person you've contacted is as ...
written 15 days ago by
Philipp Bayer ♦ 4.6k
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... To download SRA files I always use ascp, [there's a manual here][1]
It's ridiculously fast (the example command has a bandwith request of 100Mb/s, but I've used 400Mb/s before, depends on your local setup), then you can dump the fastq from the downloaded .sra file using the toolkit's `fastq-dump -- ...
written 29 days ago by
Philipp Bayer ♦ 4.6k
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... Yes, runBNG can scaffold your assembly fasta using the BioNano data, that would work!
BTW there's also OMSim, which can simulate optical mapping data from your assembly; https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx293/3791407/OMSim-a-simulator-for-optical-map-data ...
written 4 weeks ago by
Philipp Bayer ♦ 4.6k
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... So there are a few papers which did what you're trying to do.
In the goat genome paper they used both HiC and BioNano and found that HiC worked a bit better for them: http://www.nature.com/ng/journal/v49/n4/full/ng.3802.html They used Lachesis for HiC scaffolding with optimised parameters (somewher ...
written 5 weeks ago by
Philipp Bayer ♦ 4.6k
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... Having uploaded data to the SRA I never had any phenotypes for that data in the first place (but this is, in my opinion, one of the biggest problems in bioinformatics - mountains of genomic data, hills of phenotype data) ...
written 5 weeks ago by
Philipp Bayer ♦ 4.6k
2
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... SOAPaligner hasn't been updated since 2011 and still replaces N by G in alignments: https://www.biostars.org/p/101567/
But then again, I don't think people still use this aligner.
OrthoMCL seems to have a bug when calculating paralogs where it keeps self-hits - PorthoMCL (reimplementation without ...
written 5 weeks ago by
Philipp Bayer ♦ 4.6k
0
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... In WGS, you always get 5-15% unaligning reads, so I usually don't bother too much there. Not sure about the numbers for ChIP-seq... ...
written 6 weeks ago by
Philipp Bayer ♦ 4.6k
4
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... These unaligning reads could be:
- low quality reads (perhaps even containing Ns)
- lab contamination from some other species (bacteria/fungi living on your species, human preparing your samples, sequencing machine wasn't cleaned properly and you get stuff from previous runs, that's what I've seen) ...
written 6 weeks ago by
Philipp Bayer ♦ 4.6k
0
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... A few things have happened here:
1) `blast_results` is just a file handler, there are no IDs stored. So when you check whether the record ID is in the blast results all you'll check with is this thing: ``. You'll have to store the blast results in a set or a list first, like
blast_results = se ...
written 6 weeks ago by
Philipp Bayer ♦ 4.6k
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