User: jenn.drummond

gravatar for jenn.drummond
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United States
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3 years, 8 months ago
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Posts by jenn.drummond

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Should I quit PhD program?
... A couple of answers and comments have mentioned the fact that many current bioinformaticists are self-taught and do just fine. But bioinformatics graduate programs didn't exist ten or fifteen years ago when current, experienced informaticists were learning their skills. I would ask if that's still l ...
written 9 days ago by jenn.drummond30
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Comment: C: Where Can I Get The Asperasoft Command Line Client Ascp
... I don't usually indulge in thread necromancy, but I couldn't help noticing as I read this comment that it's now been 5.4 years since it was made; and we're still stuck with ascp. But hey, the browser plugin installer apparently hasn't been updated since then, so at least we can say *some* of the pes ...
written 3 months ago by jenn.drummond30
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Can't figure out order of output rows in ADMIXTURE
... Hi, all. I'm trying to do basic population structure analysis with ADMIXTURE because it's faster than STRUCTURE, but I can't figure out how to get the populations to cluster together. More generally, I can't figure out for sure what order my outputs are in, within the P and Q files. There's a [simil ...
admixture written 18 months ago by jenn.drummond30 • updated 16 months ago by beausoleilmo190
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Comment: C: Admixture cv error
... Same here. Here's some sample output from the bottom of the file. I'm not so worried about the numbers as I am about the fact that the job isn't *finishing*. It's been running for four hours and all the other versions are done, including ones with higher K values. 586 (QN/Block) Elapsed: 70.41 ...
written 18 months ago by jenn.drummond30
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Comment: C: If the index sequences in my Illumina FASTQ headers aren't the barcodes, then wh
... What a horrible thought...and therefore a useful one for the future. I'll remember that as I go through further forensics! ...
written 19 months ago by jenn.drummond30
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Comment: C: If the index sequences in my Illumina FASTQ headers aren't the barcodes, then wh
... Thanks for the excellent discussion, which I'm just now getting around to reading in detail, but continues to be relevant since I'm dealing with *several* different flavors of unpleasantly non-"standard" data. Every bit of crowdsourced clue I can get helps! This particular dataset did turn out to re ...
written 19 months ago by jenn.drummond30
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Comment: C: If the index sequences in my Illumina FASTQ headers aren't the barcodes, then wh
... Yep, you nailed it. :) ...
written 19 months ago by jenn.drummond30
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If the index sequences in my Illumina FASTQ headers aren't the barcodes, then what are they?
... Hi, everybody. I have FASTQ headers of the form @FCC3KD2ACXX:6:1101:1545:2184#ATCACGATC/1 The "ATCACGATC" portion of these older-style headers is supposed to be the "index sequence", or the molecular barcode of a multiplexed sample, according to the Wikipedia article. But I know what the barcodes ...
illumina fastq next-gen sequencing written 23 months ago by jenn.drummond30 • updated 23 months ago by harold.smith.tarheel4.1k
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Answer: A: Pindel Bad_Alloc Error With Window Size 1
... Changing from version 2.4 to version 2.5a7 stopped this problem for me. Looking at the commit messages, it does look like several memory leaks were fixed during that span of time. ...
written 3.7 years ago by jenn.drummond30
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Two undocumented fields in Pindel output
... Hi. The docs say that columns 32+ are "Per sample: the sample name, followed by the total number of supporting reads whose anchors are upstream, the total number of unique supporting reads whose anchors are upstream, the total number of supporting reads whose anchors are downstream, and finally the ...
pindel written 3.7 years ago by jenn.drummond30

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