Moderator: Chris Miller
Chris Miller ♦ 19k
- Reputation:
- 19,420
- Status:
- Trusted
- Location:
- Washington University in St. Louis, MO
- Website:
- http://chrismiller.sci...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 45 minutes ago
- Joined:
- 8 years, 3 months ago
- Email:
- c***********@gmail.com
I work in the Genome Institute at Washington University in St. Louis, where I lead a group that develops and applies computational tools to give us insight into the origins and progression of cancer.
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... really nice solution! ...
written 6 weeks ago by
Chris Miller ♦ 19k
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... Nope - the directory with the fasta and the indices was nuked. FWIW, I'm pretty sure that I can recreate this fastq by digging up the vector and gene sequences and spending an hour or two doing manual surgery. It just seems like there oughta be a better way! ...
written 6 weeks ago by
Chris Miller ♦ 19k
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... That gives each read in fasta format, not the entire contig.I guess that could be assembled in subsequent steps or something.. ...
written 6 weeks ago by
Chris Miller ♦ 19k
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6 follow
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... To make a long story short, I have a bam file that is aligned to the human reference plus a specific contig (human gene + viral vector introduced into a mouse).
The fasta file that was used for alignment got inadvertently deleted, but I have good coverage across the contig. Is there a straightfo ...
written 6 weeks ago by
Chris Miller ♦ 19k
• updated
6 weeks ago by
h.mon ♦ 15k
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... If given samtools input, copy cat will exclude chromosomes from depth normalization that appear to differ substantially from CN2, based on allele frequency information. This information is more coarse than what you'd get from programs like ABSOLUTE or TITAN_CNA, that use allele frequency but is a q ...
written 8 weeks ago by
Chris Miller ♦ 19k
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... I'd encourage you to use an existing package that rolls these normalizations in, rather than trying to reinvent the wheel. As a self-link, copyCat (https://github.com/chrisamiller/copyCat/) does mapability, GC correction, as well as normalizing global read depth. There are other tools that do simil ...
written 8 weeks ago by
Chris Miller ♦ 19k
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... You're going to want to use the` strsplit()` function with a separator of `""`. Lots of examples can be found with a few searches. ...
written 9 weeks ago by
Chris Miller ♦ 19k
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... Can you edit the question to describe what commands you used to generate the bigwig from the bam? ...
written 10 weeks ago by
Chris Miller ♦ 19k
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... Either you're going to have 0/2 copies, 1/2 copies, or 2/2 copies of that allele. ...
written 11 weeks ago by
Chris Miller ♦ 19k
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... You really need to provide more information on what kind of file format you have, but for shits and giggles, let's assume it's a bed file with the first three columns: chromsome, start, stop. Sorting is then as easy as:
sort -k 1,1 -k 2,2n myfile >outfile ...
written 3 months ago by
Chris Miller ♦ 19k
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