Moderator: Chris Miller
Chris Miller ♦ 18k
- Reputation:
- 18,180
- Status:
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- Location:
- Washington University in St. Louis, MO
- Website:
- http://www.chrisamille...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 4 hours ago
- Joined:
- 7 years, 6 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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... I'll vouch for this lab and some of the cool science they're doing! ...
written 10 weeks ago by
Chris Miller ♦ 18k
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... There may sometimes be non-reference, non-primary-variant reads - for example:
1 12345 A T Counts: A: 99 C: 2 G: 0 T: 99 VAF: 49.5%
...
written 10 weeks ago by
Chris Miller ♦ 18k
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... I suspect that using "read.table( . . . stringAsFactors=F)" will solve your problem.
(edit - it will not! see the comprehensive answer above) ...
written 3 months ago by
Chris Miller ♦ 18k
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... None of the TCGA tumors were treated prior to sequencing:
> Neoadjuvant treatment was not allowable TCGA's goal was to accelerate
> the understanding of the underlying genomics of primary, untreated
> tumors. Cancer treatment can involve mutagens or carcinogens which
> could cloud the o ...
written 3 months ago by
Chris Miller ♦ 18k
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... It sounds like one of your input files is not what you expect (and that you accidentally downloaded an html file instead of a bed file) ...
written 3 months ago by
Chris Miller ♦ 18k
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... I don't know your exact issue, but this seems to be the key line in the output:
Skipped 1054 mutation(s) that belong to unrecognized samples
Check that your sample names all match up as expected. ...
written 3 months ago by
Chris Miller ♦ 18k
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... Hello lancet_junyu!
As is, this question is unanswerable, so I'm closing it. As I told you over email, please try again, providing a detailed summary of the code you were trying to run, the output of sessionInfo(), and the output of traceback(), run just after the error occurs. Thanks ...
written 3 months ago by
Chris Miller ♦ 18k
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... bedtools intersect -a FILE1 -b <(cat FILE2 FILE3 | bedtools sort) -v >OUTFILE ...
written 3 months ago by
Chris Miller ♦ 18k
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... Your proposal of splitting into separate files by name seems reasonable to me. If that's not satisfying, nothing is stopping you from writing a 20-line perl script that does the intersection in a name-aware manner. Genome set operations aren't hard, it's just more convenient to use existing tools. ...
written 3 months ago by
Chris Miller ♦ 18k
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... In almost all cases cases, each TCGA patient only had tumor RNAseq done. ([see previous discussions][1]). Are you sure that there was actually normal RNAseq available, or have you pulled down the same file twice through different linkages?
[1]: https://www.biostars.org/p/179681/#179746 ...
written 3 months ago by
Chris Miller ♦ 18k
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