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Search: Posts Made By: priesgo
Forum: Bioinformatics 03-06-2013, 02:45 AM
Replies: 1
Views: 1,425
Posted By priesgo
I will answer myself :) A clue for this might...

I will answer myself :)
A clue for this might be that the non-matched transcripts are marked as novel in Ensemble, instead of known. So, there are two alternatives: first, that the database SnpEff...
Forum: Bioinformatics 03-01-2013, 07:41 AM
Replies: 1
Views: 1,425
Posted By priesgo
SnpEff matching policy

Hi there,

I'm digging a little bit into SnpEff and everything works fine, but I have a doubt for which I didn't find an answer in any of the SnpEff papers/documentation.
I have a variant...
Forum: Bioinformatics 02-20-2013, 06:23 AM
Replies: 2
Views: 1,272
Posted By priesgo
Thumbs up Thanks! Yes that's it I hadn't realized it...

Thanks!
Yes that's it I hadn't realized it gave you the partial overlaps .
Forum: Bioinformatics 02-20-2013, 03:13 AM
Replies: 2
Views: 1,272
Posted By priesgo
Tabix index at contig, start and end??

Hi there,

I have indexed a tab separated file using tabix. In order to do so, I gave tabix the indexes of the columns for the contig, the start position and the end position (let's call these the...
Forum: Bioinformatics 01-22-2013, 12:10 AM
Replies: 5
Views: 1,665
Posted By priesgo
Thanks again Justin, Yes, it seems to be an...

Thanks again Justin,

Yes, it seems to be an issue with the original file, don't know if coming from mosaik or somewhere else.

Pablo.
Forum: Bioinformatics 01-21-2013, 01:53 AM
Replies: 5
Views: 1,665
Posted By priesgo
Thanks for your answers! maubp, I am using...

Thanks for your answers!
maubp, I am using version 1.00-b244 and it is linked to Picard 1.79.
Justin, this data is an Illumina exome from the 1000 Genomes Project. As it is reported in the project...
Forum: Bioinformatics 01-17-2013, 02:49 AM
Replies: 5
Views: 1,665
Posted By priesgo
CRAM compression and TLEN SAM's field

Hi there,

I'm evaluating the CRAM compression. So, I'm comparing the same BAM sample pre and post CRAM compression.

I found that in my data the TLEN (Template Length) field is sistematically...
Forum: Bioinformatics 01-16-2013, 08:05 AM
Replies: 37
Views: 8,080
Posted By priesgo
It was not my intention to make of this a...

It was not my intention to make of this a discussion about Integromics or Spotfire software, it was just an example to justify the use of commercial software for a biomedical researcher with no...
Forum: Bioinformatics 01-16-2013, 04:21 AM
Replies: 11
Views: 2,346
Posted By priesgo
You have the fishing cane now! Just fish it! :)

You have the fishing cane now! Just fish it! :)
Forum: Bioinformatics 01-16-2013, 04:13 AM
Replies: 11
Views: 2,346
Posted By priesgo
You are right, I didn't know it will match...

You are right, I didn't know it will match incomplete lines like that. Nice!
Forum: Bioinformatics 01-16-2013, 03:58 AM
Replies: 11
Views: 2,346
Posted By priesgo
I modified your data a little bit to have some...

I modified your data a little bit to have some output.
File1:
Pc_TC00002
Pc_TC00004
Pc_TC51641
Pc_TC00009
Pc_TC51668
Pc_TC00045
Pc_TC51688
Forum: General 01-16-2013, 02:59 AM
Replies: 16
Views: 11,289
Posted By priesgo
Thanks Bruce, It's running! For the...

Thanks Bruce,

It's running!
For the columns 12+ I guess with the option --capture-tags you can keep tags as the read group which is usually important.


Regards,
Pablo.
Forum: Bioinformatics 01-16-2013, 02:19 AM
Replies: 37
Views: 8,080
Posted By priesgo
In my honest opinion if you are doing biomedical...

In my honest opinion if you are doing biomedical research and you don't have bioinformaticians around and you are not planning to create a whole department it would be better to go for commercial...
Forum: Bioinformatics 01-16-2013, 01:56 AM
Replies: 11
Views: 2,346
Posted By priesgo
Hi there, You can first join the two files...

Hi there,

You can first join the two files in the id column. Something like:
join -j your_id_column file1 file2 > file3

And then substract this result from the original with grep. Something...
Forum: General 01-16-2013, 01:46 AM
Replies: 16
Views: 11,289
Posted By priesgo
Hi, I'm in the same situation as Bruce. I...

Hi,

I'm in the same situation as Bruce. I want to compress keeping the base call qualities but can't figure out how...

Just did a naf try:--lossy-quality-score-spec all
and got:
Exception in...
Forum: Bioinformatics 01-02-2013, 06:03 AM
Replies: 8
Views: 3,933
Posted By priesgo
Let me retake this old issue. I am working...

Let me retake this old issue.

I am working with 1000 genomes project alignments data and they have done their SOLiD alignment with bfast 0.64e, so I have two options: I redo the alignment myself...
Forum: Genomic Resequencing 12-14-2012, 10:42 PM
Replies: 12
Views: 6,233
Posted By priesgo
gsgs I am trying to process this data using...

gsgs I am trying to process this data using existing tools as vcftools I am avoiding getting into the guts of it. Anyway this may apply to optimize vcftools.
Forum: Genomic Resequencing 12-14-2012, 01:43 AM
Replies: 12
Views: 6,233
Posted By priesgo
Mmmmm, sorry I didn't explain well myself. ...

Mmmmm, sorry I didn't explain well myself.

Yes I was referring to Next Generation Sequencing. The thing is that the OMNI data you proposed is obtained via Illumina OMNI microarray genotyping,...
Forum: Genomic Resequencing 12-14-2012, 12:35 AM
Replies: 12
Views: 6,233
Posted By priesgo
Thanks gsgs, It seems a good alternative, but...

Thanks gsgs,
It seems a good alternative, but in my case I need data from NGS.

By the way I launched yesterday an script like the one cwhelan proposed and it is now with the chromosome 15 and it...
Forum: Genomic Resequencing 12-13-2012, 05:00 AM
Replies: 12
Views: 6,233
Posted By priesgo
HI there, What is the 2123???

HI there,

What is the 2123???
Forum: Genomic Resequencing 12-13-2012, 04:31 AM
Replies: 12
Views: 6,233
Posted By priesgo
Hi, Thanks for your response! I...

Hi,


Thanks for your response!
I actually was wrong with the code I posted, I am already executing vcf-subset with -e and -a and I'm already not using tabix. So, we are at the same point.

I...
Forum: Genomic Resequencing 12-12-2012, 09:00 AM
Replies: 12
Views: 6,233
Posted By priesgo
Select only one sample in 1000 Genomes whole genome VCF

Hi there,

First of all I have to say how incredible is the work people is doing at 1KG project. This post is not to criticize their work, but just to ask for some insight into how to best use...
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