User: laura

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laura0
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Posts by laura

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Comment: C: DNA intervals start stop
... zero based meaning the first base is numbered 0 (not 1), and exclusive meaning that the "stop" base is not included. ...
written 2.9 years ago by laura0
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Comment: C: DNA intervals start stop
... That appears to have been my situation. Thanks for the explanation. Laura Georgi American Chestnut Foundation Meadowview Research Farms 29010 Hawthorne Dr Meadowview, VA 24361 tel 276-944-4631 fax 276-944-0934 laura@acf.org ...
written 2.9 years ago by laura0
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DNA intervals start stop
... I just ran extract genomic DNA using an interval file with start and stop calculated from SNP positions as plus and minus 200. This returned 400 bases of sequence; I was expecting 401. Does the sequence start at START, or at START+1? Thanks Laura ...
galaxy written 2.9 years ago by laura0 • updated 2.9 years ago by Hotz, Hans-Rudolf1.7k
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Answer: A: GATK indel realigner using custom reference
... Thanks, Jen. I vaguely remembered that the reference needed something done to it, but was perplexed that the problem only surfaced with the downstream tool. I'll try sorting. Laura ...
written 3.4 years ago by laura0
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GATK indel realigner using custom reference
... I've been using some SAM (converted to BAM) files and some partial genome assemblies (custom reference sequences) to investigate variants in bulk sequences. GATK's rmdup and Realigner Target Creator had no problem with the files, but when I used them and the output of Realigner Target Creator in Ind ...
indel realigner custom reference gatk written 3.4 years ago by laura0 • updated 17 months ago by vignes.gangboard0

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