User: igor
igor • 4.4k
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Posts by igor
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3
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answer
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... There are instructions given in the [VarScan documentation][1] for extracting somatic mutations:
> The latest release of VarScan includes a new (undocumented) subcommand
> that will separate a somatic output file by somatic_status (Germline,
> Somatic, LOH). Somatic mutations will further ...
written 29 days ago by
igor • 4.4k
1
vote
1
answer
625
views
1
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... I don't think they check the contents of your files other than to make sure they are in the proper format. ...
written 29 days ago by
igor • 4.4k
0
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3
answers
386
views
3
answers
... See also: https://www.glassdoor.com ...
written 7 weeks ago by
igor • 4.4k
2
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2
answers
1.2k
views
2
answers
Comment:
C: 10x Supernova de novo assembly
... More importantly, they came out with a new version of the reagents (v2). We had multiple failed assemblies with v1, but all worked with v2. ...
written 7 weeks ago by
igor • 4.4k
1
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1
answer
228
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1
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... Keep it mind that the original reference human genome was completed in 2003. Many people have been working on improving it ever since, so it's a lot of work. ...
written 8 weeks ago by
igor • 4.4k
1
vote
5
answers
2.5k
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5
answers
... Good find. However, the paper mostly discusses single-cell RNA-seq.
Regarding normal bulk RNA-seq, they say:
> In the Illumina labs, the team also experimented with purposefully
> generating a large number of PCR duplicates. The team compared data
> from unique reads and duplicates—'good' ...
written 8 weeks ago by
igor • 4.4k
1
vote
3
answers
318
views
3
answers
Comment:
C: FASTQ to SAM File converter
... Definitely faster than some of those fancy aligners. ...
written 9 weeks ago by
igor • 4.4k
0
votes
1
answer
155
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1
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... Thanks for confirming. I just wanted to make sure I am not reinventing the wheel or missing something. ...
written 9 weeks ago by
igor • 4.4k
2
votes
3
answers
318
views
3
answers
Comment:
C: FASTQ to SAM File converter
... You should figure out exactly what you are trying to do and understand the whole process before trying to find "the fastest tools". ...
written 9 weeks ago by
igor • 4.4k
1
vote
1
answer
155
views
1
answer
... I recently found ReMap which is a great resource of TF binding sites across different studies. They [provide][1] the binding sites in BED format where each region is named based on the TF. Although it's relatively trivial to overlap two BED files (using something like `bedtools fisher` or `bedtools ...
written 9 weeks ago by
igor • 4.4k
• updated
9 weeks ago by
Chris Miller ♦ 18k
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