User: Sander

gravatar for Sander
Sander20
Reputation:
20
Status:
New User
Location:
The Netherlands
Website:
http://www.thehyve.nl/
Last seen:
1 year, 10 months ago
Joined:
5 years, 3 months ago
Email:
t********@gmail.com

Posts by Sander

<prev • 4 results • page 1 of 1 • next >
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Answer: A: Making TSS plots for some genes for a particular histone mark
... Also NGS-Plot is a nice tool! https://github.com/shenlab-sinai/ngsplot ...
written 4.8 years ago by Sander20
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Answer: A: ChIP-Seq alignment with random site for duplicated
... Hi, I can recommend Bowtie1 for this purpose. It has an option for exactly what you want: -m suppress all alignments if > exist (def: no limit) So in your case, you want to set `-m 1` I don't have experience with Bowtie2, (I've looked in the help but couldn't find a similar opt ...
written 4.9 years ago by Sander20 • updated 6 months ago by RamRS27k
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Comment: C: Bowtie: Reporting one of multiple valid mapping locations
... So with -k 1, in the case that a read maps to various places, which position is reported? ...
written 5.3 years ago by Sander20
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Bowtie: Reporting one of multiple valid mapping locations
... Dear Biostars, I'm slightly confused by the way Bowtie reports reads that align to multiple locations. If I understand correctly from the manual, http://bowtie-bio.sourceforge.net/manual.shtml#reporting , by default only 1 alignment is returned (-k 1). But this may not necessarily be the best align ...
mapping bowtie written 5.3 years ago by Sander20 • updated 5.3 years ago by geek_y11k

Latest awards to Sander

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Bowtie: Reporting one of multiple valid mapping locations
Scholar 4.9 years ago, created an answer that has been accepted. For A: ChIP-Seq alignment with random site for duplicated

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