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Search: Posts Made By: francois.sabot
Forum: Bioinformatics 02-27-2013, 02:12 AM
Replies: 23
Views: 4,400
Posted By francois.sabot
What about a simple grep ? grep 'chr1' FILE...

What about a simple grep ?

grep 'chr1' FILE > chr1.txt
grep 'chr2' FILE > chr2.txt
Forum: General 03-30-2012, 03:43 AM
Replies: 23
Views: 6,358
Posted By francois.sabot
Try Linux ^^

Try Linux ^^
Forum: Introductions 03-30-2012, 03:40 AM
Replies: 2
Views: 1,011
Posted By francois.sabot
Incredible, Perpignan PhD in SEQ answers ^^ ...

Incredible, Perpignan PhD in SEQ answers ^^

Cheers to Marion
Forum: Bioinformatics 12-12-2011, 12:26 AM
Replies: 0
Views: 2,173
Posted By francois.sabot
VariantFiltration weird error

Hi everyone
It was a long time since I do not have a bug...

I was trying to filter my raw vcf data (both SNP and InDel in the same file, all sites emited), from rice (plant...), and I use this...
Forum: General 09-14-2011, 01:46 AM
Replies: 2
Views: 4,802
Posted By francois.sabot
Hi One overcome for that is to generate a VCF...

Hi
One overcome for that is to generate a VCF file from BAM and then extrapolate your sequence based on your ref. We have performed that using a simple home-made script and VCF file with all site...
Forum: Bioinformatics 06-28-2011, 08:16 AM
Replies: 3
Views: 4,123
Posted By francois.sabot
Converting VCF to GFF (again)

Hi folks,
I know the question was already asked here (as in http://seqanswers.com/forums/showthread.php?t=9796&highlight=gff+vcf)..

But my problem is that the data I have are on plants, and are...
Forum: Bioinformatics 06-08-2011, 11:45 PM
Replies: 6
Views: 23,391
Posted By francois.sabot
Yes it is redundant at first look, but if you did...

Yes it is redundant at first look, but if you did not specified the RG tag during the mapping assay (as BWA allows eg), you did not have this information within the SAM file. Thus you need to add it,...
Forum: Bioinformatics 06-08-2011, 12:49 AM
Replies: 6
Views: 23,391
Posted By francois.sabot
The origin in my case can be either a lane, the...

The origin in my case can be either a lane, the name of the individual/organism. You can have eg 10 individuals tagged in a single lane, then mapped individually and then affected to a group (eg...
Forum: Bioinformatics 06-08-2011, 12:07 AM
Replies: 6
Views: 23,391
Posted By francois.sabot
A ReadGroup will assign an origin to a set of...

A ReadGroup will assign an origin to a set of reads in order to assign a specific genotype to this origin when making the SNP/InDel calling. Without this step, you will have a set of SNPs but you...
Forum: General 06-08-2011, 12:04 AM
Replies: 2
Views: 1,932
Posted By francois.sabot
Hi, you can probably sort them by coordinatées...

Hi,
you can probably sort them by coordinatées using the Picardtools Samtools, and then using home-made scripts or an alternate use of Depth-of-Coverage to determinate the positions with such high...
Forum: Bioinformatics 05-13-2011, 05:37 AM
Replies: 4
Views: 2,167
Posted By francois.sabot
Hi Have a look at the last version of Cutadapt,...

Hi
Have a look at the last version of Cutadapt, which uses a nice system for trimming, and cut only if the fater bases are of better quality than the previous... See their explanation :...
Forum: Illumina/Solexa 03-11-2011, 12:09 AM
Replies: 8
Views: 10,177
Posted By francois.sabot
In fact those specs came from my classical...

In fact those specs came from my classical provider (Integragen, France), from their own experience... No paper associated with so. Sorry :s
Forum: Bioinformatics 12-23-2010, 02:15 AM
Replies: 14
Views: 9,688
Posted By francois.sabot
From...

From http://lj4newbies.blogspot.com/2007/04/too-many-open-files.html (first google results for Java Too Many open Files)



So, the descriptors seem to be too numerous
Forum: Bioinformatics 10-27-2010, 07:54 AM
Replies: 8
Views: 1,552
Posted By francois.sabot
Switch to linux... Ok, I left. No sorry, no...

Switch to linux... Ok, I left.

No sorry, no idea :s
Forum: Bioinformatics 10-27-2010, 07:48 AM
Replies: 8
Views: 1,552
Posted By francois.sabot
Try to install them directly from your system...

Try to install them directly from your system (yuml, aptitude, apt-get, etc..)
or ask the administrator if you do not have the right...
Forum: Bioinformatics 10-27-2010, 07:46 AM
Replies: 14
Views: 9,688
Posted By francois.sabot
No more space in the hard drive ?

No more space in the hard drive ?
Forum: General 10-25-2010, 02:19 AM
Replies: 4
Views: 5,125
Posted By francois.sabot
Check also Paux et al, Science (2007 ?). They...

Check also Paux et al, Science (2007 ?). They have isolated the 3B chromosome of bread wheat (~800 Mb) and performed a BAC library with. They recently also made a NGS (solexa) analysis on this...
Forum: Bioinformatics 10-22-2010, 12:30 AM
Replies: 2
Views: 1,812
Posted By francois.sabot
Here it is ^^ http://seqanswers.com/wiki/ABySS ...

Here it is ^^
http://seqanswers.com/wiki/ABySS

Try to check in the webpage links for more Infos.

Cheers

Francois
Forum: Bioinformatics 10-21-2010, 04:26 AM
Replies: 3
Views: 1,993
Posted By francois.sabot
LASTZ has a specific module to perform...

LASTZ has a specific module to perform exomapping, called FEAST..;

See http://www.ncbi.nlm.nih.gov/pubmed/20733242

Either use BWA (which accept more SNPs than bowtie and can manage indels)...
Forum: General 10-18-2010, 12:40 AM
Replies: 2
Views: 2,422
Posted By francois.sabot
This amount of 'x' depend also of the size of...

This amount of 'x' depend also of the size of your reads: longer reads need less coverage for the same efficiency
Forum: General 10-14-2010, 01:24 AM
Replies: 11
Views: 3,983
Posted By francois.sabot
I may say that BWA accepts indel...

I may say that BWA accepts indel...
Forum: Bioinformatics 10-11-2010, 12:52 AM
Replies: 1
Views: 1,763
Posted By francois.sabot
Are you sure there are only miRNA, and not...

Are you sure there are only miRNA, and not si/tasiRNA, targetting the repeats, in your sample ?
Forum: Illumina/Solexa 10-07-2010, 01:53 AM
Replies: 5
Views: 3,337
Posted By francois.sabot
Check this page, containing all the Solexa...

Check this page, containing all the Solexa adapters:

http://intron.ccam.uchc.edu/groups/tgcore/wiki/013c0/Solexa_Library_Primer_Sequences.html
Forum: Bioinformatics 10-07-2010, 01:49 AM
Replies: 11
Views: 13,294
Posted By francois.sabot
There is also cutadapt, allowing a % of...

There is also cutadapt, allowing a % of distance..
in fastx_clipper, you can specify the -M value lower than your adapter size, for the bording mutation. Just remind that fastx_clipper remove one by...
Forum: Bioinformatics 10-05-2010, 02:40 AM
Replies: 3
Views: 5,582
Posted By francois.sabot
Either, put all the files in the same folder, and...

Either, put all the files in the same folder, and then launch the following command:



All your fasta files will be written in complete_bos.fasta and the formatting will be performed after.
...
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