User: blair

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blair20
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Location:
Cambridge, MA
Website:
http://www.sbgenomics.com
Last seen:
7 years, 2 months ago
Joined:
8 years, 3 months ago
Email:
b****@sbgenomics.com

Swan diving into the world of deep sequencing. Cell biologist by training.

Posts by blair

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Comment: C: Presets And Dependent Parameters For Bowtie2/Tophat2
... Thanks seidel. Implemented suggestion 1. Will probably go for option 2 when I get some spare time. Will surely report back when I sort it out. ...
written 7.5 years ago by blair20
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Comment: C: Presets And Dependent Parameters For Bowtie2/Tophat2
... Hey all, sorry for the confusing question. Hope I can clarify. There are the four preset options (fast, very fast, sensitive, very sensitive). So if I run bowtie2 --very sensitive, it will set the following parameters ( -D 20 -R 3 -N 0 -L 20 -i S,1,0.50. ). But what if I enter bowtie2 --very sensiti ...
written 7.5 years ago by blair20
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Presets And Dependent Parameters For Bowtie2/Tophat2
... [Edited for clarity]. If you enter a preset option and its dependent parameters in Bowtie or TopHat, which one will override and be implemented? For example, there are the four preset options (fast, very fast, sensitive, very sensitive). So if I run bowtie2 --very sensitive, it will set the followin ...
bowtie2 tophat2 written 7.5 years ago by blair20 • updated 6.7 years ago by Biostar ♦♦ 20
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Answer: A: What Kind Of Inputs Does Cuffdiff Take?
... The BED output files produced by TopHat are for those interested in discovering new transcripts and splice-junctions. For a DE experiment using samples from an organism with a well annotated genome (like human or mouse) then your best bet is to just take your accepted_hits.bam from TopHat and input ...
written 7.6 years ago by blair20

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