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Forum: Bioinformatics 11-20-2015, 04:38 AM
Replies: 5
Views: 2,567
Posted By MurielGB
So, if I understand well, this command...

So, if I understand well, this command "--non-ref-ac 1" allows to remove sites where there is no alternative allele at all ?

That's what I want to do, since I filtered out some individuals in my...
Forum: Bioinformatics 11-20-2015, 04:16 AM
Replies: 5
Views: 2,567
Posted By MurielGB
Thanks Mastral, I checked the manual before...

Thanks Mastral, I checked the manual before asking the quetsion ;)
But I don't understand what this means...
Sorry.
Forum: Bioinformatics 11-20-2015, 01:35 AM
Replies: 5
Views: 2,567
Posted By MurielGB
Vcftools option --non-ref-ac

Hello !

Can someone explain the --non-ref-ac option ?

I don't manage to get it :confused:

What happened if I do:
vcftools --vcf input.vcf --non-ref-ac 1 --out outout --recode

Thanks !!!
Forum: Bioinformatics 10-28-2014, 06:30 AM
Replies: 0
Views: 1,184
Posted By MurielGB
Training Augustus with RNA seq data

Hello all,
I am trying to annotate a genome (476 Mb ; 8,000 scaffolds).
I plan to use the Maker pipeline and before that, I need to train Augustus.
I have plenty of RNA seq data that I mapped and...
Forum: Illumina/Solexa 10-07-2014, 07:39 AM
Replies: 9
Views: 2,595
Posted By MurielGB
OK, thanks a lot !

OK, thanks a lot !
Forum: Illumina/Solexa 10-07-2014, 07:31 AM
Replies: 9
Views: 2,595
Posted By MurielGB
OK but when I do fastqc on the fastq file with...

OK but when I do fastqc on the fastq file with 101bp reads, I obtain the attached graph that is, to me, typical of problems of read splitting with bad length.
Forum: Illumina/Solexa 10-07-2014, 07:19 AM
Replies: 9
Views: 2,595
Posted By MurielGB
Yeah I agree but then why do I obtain 152bp reads...

Yeah I agree but then why do I obtain 152bp reads when using fastq-dump ?!!
Forum: Illumina/Solexa 10-07-2014, 07:11 AM
Replies: 9
Views: 2,595
Posted By MurielGB
I don't know if this is possible. When I...

I don't know if this is possible.
When I convert SRA to FASTQ without any option, I obtain a fastq with 152bp reads.

Here is the page where I downloaded the sra file :...
Forum: Illumina/Solexa 10-07-2014, 07:05 AM
Replies: 9
Views: 2,595
Posted By MurielGB
Convert SRA to FASTQ with fastq-dump but problem of read length

Hello,
I have Illumina paired end reads of length 76bp.
The problem is that when I use fastq-dump to obtain two files with paired reads separated, it splits the reads into 101bp and 51bp rather...
Forum: Bioinformatics 05-28-2014, 11:59 PM
Replies: 3
Views: 2,523
Posted By MurielGB
Hi all ! Thanks a lot for your answers. ...

Hi all !

Thanks a lot for your answers.
Lindenb, I would like to use your tool but don't manage to install it...

I tried to follow the installation but it doesn't work.

I did :
git clone...
Forum: Bioinformatics 05-28-2014, 06:21 AM
Replies: 3
Views: 2,523
Posted By MurielGB
Downsample vcf file

Hello !

Is there a tool available to randomly select let's say 1,000 snps in a vcf file ?
Thank you !

Muriel
Forum: Bioinformatics 05-09-2014, 01:00 AM
Replies: 9
Views: 2,912
Posted By MurielGB
Hello ! Well, what I did is a personal...

Hello !
Well, what I did is a personal arrangement. I should probably write to the mailing list, I don't remember if I did or not ahah !!
The problem is that some read are supposedly mapped on the...
Forum: Bioinformatics 05-06-2014, 07:01 AM
Replies: 14
Views: 4,492
Posted By MurielGB
I have another problem, sorry vdauwera :( I...

I have another problem, sorry vdauwera :(

I did variant calling on two samples individually using the option described and it works well, I have both variant and invariant sites.

However, the...
Forum: Bioinformatics 05-05-2014, 10:01 PM
Replies: 14
Views: 4,492
Posted By MurielGB
So cooool !!! Thanks a lot, I am very happy of...

So cooool !!!
Thanks a lot, I am very happy of this new tool, it's gonna allow population geneticists to do so much !
Forum: Bioinformatics 05-05-2014, 12:49 AM
Replies: 14
Views: 4,492
Posted By MurielGB
Well... I am wondering if I won't have another...

Well... I am wondering if I won't have another problem using -ERC BP_RESOLUTION.
Because after that I obtain a vcf file per sample containing both variant and invariant sites, I want to run the...
Forum: Bioinformatics 05-04-2014, 10:48 PM
Replies: 14
Views: 4,492
Posted By MurielGB
Oh great !! I was wondering what was the...

Oh great !!
I was wondering what was the difference between these two options !
Thanks a lot for your help vdauwera !
Forum: Bioinformatics 05-04-2014, 12:52 AM
Replies: 14
Views: 4,492
Posted By MurielGB
Hi ! I had a look on this new pipeline. ...

Hi !

I had a look on this new pipeline.

I launched variant calling on a bam file containing only one sample with the options mentioned before :


I still don't have all positions in the...
Forum: Bioinformatics 05-02-2014, 08:53 AM
Replies: 14
Views: 4,492
Posted By MurielGB
Thank you cariboudoug ! Indeed, I tried this...

Thank you cariboudoug !
Indeed, I tried this already but I was thinking that it's probably better to use HaplotypeCaller since this is the new version of UnifiedGenotyper...
Forum: Bioinformatics 05-02-2014, 08:28 AM
Replies: 14
Views: 4,492
Posted By MurielGB
Hi, Thank you vdauwera for your answer. The...

Hi,
Thank you vdauwera for your answer.
The thing is that when you do that, you can't have a bam containing multiple samples.
Muriel
Forum: Bioinformatics 05-02-2014, 02:03 AM
Replies: 14
Views: 4,492
Posted By MurielGB
Calling invariant sites with GATK

Hello,

I would like to obtain a vcf with variant AND INVARIANT sites using GATK.
I am not sure about the options to use in order to obtain invariant sites.
I tried a few but still I have only...
Forum: Bioinformatics 05-01-2014, 02:03 AM
Replies: 16
Views: 2,360
Posted By MurielGB
If I understand well, I need to split my fastq...

If I understand well, I need to split my fastq files because for the short reads I will use bbmap.sh while for the longest ones I need to use mapPacBio8k.sh ?
I checked and I have reads from 45 to...
Forum: Bioinformatics 04-30-2014, 09:26 AM
Replies: 16
Views: 2,360
Posted By MurielGB
What is the output of BBMap ? I want then to...

What is the output of BBMap ?
I want then to use Cufflink, is it ok ?
Forum: Bioinformatics 04-30-2014, 09:22 AM
Replies: 16
Views: 2,360
Posted By MurielGB
Sorry, I meant FastQ format...

Sorry, I meant FastQ format...
Forum: Bioinformatics 04-30-2014, 09:20 AM
Replies: 16
Views: 2,360
Posted By MurielGB
OK thank you, I didn't know this software, I'll...

OK thank you, I didn't know this software, I'll have a look on it !

I wanted to use Tophat since I also have Illumina RNA-seq and for these ones I used Tophat and I thought, it would be cool to...
Forum: Bioinformatics 04-30-2014, 09:10 AM
Replies: 16
Views: 2,360
Posted By MurielGB
My data are in fast format. It seems that...

My data are in fast format.
It seems that length are from 60 to 900 bp...

I haven't trim on quality and length, maybe I should ? Which tool to use ? I used Sickle for another project with...
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