User: Wolf

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Wolf130
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Posts by Wolf

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Ion Torrent Transcriptome Data Sets?
... i completely read over the transcriptome part of the question... sorry ...
written 8.2 years ago by Wolf130
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Answer: A: Ion Torrent Transcriptome Data Sets?
... SRA has a few public data sets: http://www.ncbi.nlm.nih.gov/sra?term=Ion%20Torrent including the whole human genomes published recently (http://www.ncbi.nlm.nih.gov/pubmed?term=21776081): http://www.ncbi.nlm.nih.gov/sra/ERX016676 ...
written 8.2 years ago by Wolf130 • updated 5 months ago by RamRS25k
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Answer: A: Using A Patient'S Social Network To Diagnose Disease
... maybe this study on military personel: http://www.ncbi.nlm.nih.gov/pubmed/17760855 ...
written 8.2 years ago by Wolf130
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Answer: A: Closest (Distance, Bp) Promotor To A Snp
... bedtools (http://code.google.com/p/bedtools/) closestBed will do what you need ...
written 8.2 years ago by Wolf130
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Comment: C: How To Convert A Basic Bed File With Only 3 Columns (Chrname, Start, End Site) I
... it means that you can't ask MACS to estimate ChIP fragment size from the data (i.e. use --no-model). Usually you would use the fragment size to shift/extend plus strand reads to the right and minus strand reads to the left, so that the cover the actual binding site that was pulled down. You won't ...
written 8.2 years ago by Wolf130
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Answer: A: How To Convert A Basic Bed File With Only 3 Columns (Chrname, Start, End Site) I
... MACS uses strand information (which would be in column 6) for the fragment size model it builds. If you want to use MACS and you expect your peaks to be narrow (i.e. you would want to use the model building step), I think you should try to get the strand information from whatever aligner you used i ...
written 8.2 years ago by Wolf130
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Comment: C: Structural Variation Detection On A Short Reads Simulation
... but bowtie1 does not do gapped alignment, so there won't be any reads spanning your indels ...
written 8.3 years ago by Wolf130
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Answer: A: Structural Variation Detection On A Short Reads Simulation
... I may be missing something very basic here, but are you sure you are actually using bowtie2 and not bowtie1? the executables are bowtie2 and bowtie2-align and i think bowtie2 takes it's index with the -x switch. ...
written 8.3 years ago by Wolf130

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