User: Siva

gravatar for Siva
Siva20
Reputation:
20
Status:
New User
Location:
France
Last seen:
3 years, 6 months ago
Joined:
5 years, 3 months ago
Email:
n**********@gmail.com

I'm a bioinformaticien, working on NGS data, so often making mapping and assembly.

Posts by Siva

<prev • 27 results • page 1 of 3 • next >
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genomeCoverageBed out > mapping out
... Hello guys, An other doubt today ;) Got a bwa sam file results from a mapping of single reads, I have in my sam file 33 results, means 33 of my reads into 33 reads have been mapped, no overlap between reads and just uniquely mapped reads. So I expected to have 33 lines in my output file from "geno ...
bedtools genomecoveragebed bwa sam written 3.6 years ago by Siva20 • updated 3.3 years ago by James Ashmore2.5k
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Comment: A: ordered genome ?
... Ok thanks guys. I think chromosomes are conserved in the genome, i'll continue with that. ps: I don't want to change the order, just wanted to confirm the real order in the real genome.   ...
written 3.6 years ago by Siva20
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Comment: C: ordered genome ?
... Nope airan I can't make a bedtools because haven't got bed file, and i don't want to retrieve sequences. The file I give before is already from samtools faidx so no use to take that to make a getfasta. I just want to know if the genome I have is already a contiguous one so with a good order of his c ...
written 3.6 years ago by Siva20
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Comment: C: ordered genome ?
... yea when I did a grep I got the same order than in this file : https://gist.github.com/anonymous/aca071080e964f878087 The question is: so in my genome the order of the chromosomes is what it's given by the grep result ? It could not be an other order ? In the real genome we'll find it in that order ...
written 3.6 years ago by Siva20
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Comment: C: ordered genome ?
... I search a way to know if chromosomes of my genome are in this order. Actually I got a genome file, and wanted to locate some genes and retrieve the part of the genome, but before that I should know if my genome has already ordered chromosomes. ...
written 3.6 years ago by Siva20
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ordered genome ?
... Hi friends,  Got a small doubt about a genome file. I don't know if my chromosomes are already ordered in my fasta file ? --" Actually I think it is because it's not 1 to 17.   Just want to confirm with you before to extract the region I wanted after a blast. My indexed genome order: https://gist. ...
genome order blast chromosomes written 3.6 years ago by Siva20 • updated 3.6 years ago by Alex Reynolds26k
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Comment: C: abyss-pe file prob double /1
... Hi Benv, i'll not try with PE only because I wanted to make contigs with single end reads also. Then yea I also think that problem is coming from my files, I got it from a "bwa mem" mapping and so have none unique alignement that's why having multiple /1 or multiple /2.  But I've made a filtering b ...
written 3.6 years ago by Siva20
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Comment: C: abyss-pe file prob double /1
... I got these files, but not final contig file : coverage.hist mappedR_XRQrefSF099_SEPE-bubbles.fa mappedR_XRQrefSF099_SEPE-1.fa mappedR_XRQrefSF099_SEPE-1.adj mappedR_XRQrefSF099_SEPE-2.adj mappedR_XRQrefSF099_SEPE-1.path mappedR_XRQrefSF099_SEPE-3.adj mappedR_XRQrefSF099_SEPE-2.path mappedR_XRQrefS ...
written 3.6 years ago by Siva20
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abyss-pe file prob double /1
... Hi guys,  I really don't understand, always got a problem to make an abyss with real data :( Got this in my log (full log here : https://gist.github.com/anonymous/909f5f5b059f8ef6b589):  abyss-map: missing arguments abyss-fixmate: error: All reads are mateless. This can happen when first and secon ...
assembly paired-end abyss written 3.6 years ago by Siva20 • updated 3.6 years ago by benv710
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Comment: C: correct fastq file with SED
... nope it's not the last line, here for the example yea but in my real data not. ...
written 3.6 years ago by Siva20

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