User: vimartin

gravatar for vimartin
vimartin30
Reputation:
30
Status:
New User
Location:
France
Last seen:
3 years, 3 months ago
Joined:
3 years, 8 months ago
Email:
v**************@curie.fr

Posts by vimartin

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Adquate tool for mapping to a short reference
... Hi, Thanks for your answer. In fact I'm more concerned about speed, and I was wondering whether I some other tools could be faster than classic aligners? ...
written 3.4 years ago by vimartin30
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Adquate tool for mapping to a short reference
... Hi, I have to repetitively perform an alignment task of reads to short (few hundreds bp) references. I intended to use bwa mem but I'm wondering if there is any tool which is more suited for this task, I only found a discussion (http://seqanswers.com/forums/showthread.php?t=9900) on this subject fr ...
alignment next-gen written 3.4 years ago by vimartin30 • updated 3.4 years ago by Istvan Albert ♦♦ 77k
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Answer: A: bwa mem on a bam file
... Ok, I should have wait I guess. Finally I found the answer which is : no.  This was detailed in the mail archive announcing the release of bwa mem. I put it as an answer in case someone else ask himself the same question. http://sourceforge.net/p/bio-bwa/mailman/message/30527151/ ...
written 3.4 years ago by vimartin30
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bwa mem on a bam file
... Hi, I'm trying to use bwa mem for the first time and I wonder, is it possible to run it on a bam file instead of a fastq file? I noticed that bwa aln can be runned on bam file using '-b' but this option is invalid for bwa mem. The manual does not mention whether it is possible or not. I tried to si ...
bwa-mem ngs bam written 3.4 years ago by vimartin30 • updated 2.1 years ago by Biostar ♦♦ 20
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Comment: C: MatePosition & InsertSize in Bamtools
... Thanks a lot for all your quick and precise answers :-). ...
written 3.5 years ago by vimartin30
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Comment: C: MatePosition & InsertSize in Bamtools
... Ok, I thought (at least it seems true on the file I'm parsing) that it was always in terms of genomic coordinates. Is there a complete specification of Bam/Sam format more precise than this one http://samtools.github.io/hts-specs/SAMv1.pdf in which I cannot find the definition of the insertSize of t ...
written 3.5 years ago by vimartin30
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Comment: C: MatePosition & InsertSize in Bamtools
... Thank for your answer. To be clear, when you say that if they span a (normal) splicing event the insertsize might be unreliable, you mean that it is unreliable for determining the actual insert size of the RNA fragment red or that we can't still have the genomic end position of the mate using it?  ...
written 3.5 years ago by vimartin30
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MatePosition & InsertSize in Bamtools
... Hi, I'm currently using BamTools to parse a (paired-end) RNA-seq bam file for detecting possible chimera.  I'm focusing on reads where both pairs belong to different genes but I have a hard time to understand some of the BamTools::BamAlignment members.  For example, it is easy to get the starting ...
chimera bamtools rna-seq written 3.5 years ago by vimartin30 • updated 3.5 years ago by Devon Ryan82k

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Scholar 3.4 years ago, created an answer that has been accepted. For A: bwa mem on a bam file

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