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Search: Posts Made By: albireo
Forum: Bioinformatics 08-21-2014, 07:13 AM
Replies: 1
Views: 3,141
Posted By albireo
Alternative to SNAP (Broad) for finding SNPs in LD to initial set?

Hi

I have a list of SNPs and would like to recover all SNPs in strong LD with them (let's say 0.9) within a population (for example CEPH).

There is a web interface which does this (SNAP by...
Forum: Bioinformatics 03-04-2014, 04:20 AM
Replies: 4
Views: 1,321
Posted By albireo
I was going through a hardcopy version of the...

I was going through a hardcopy version of the vignette and the line you mention is not there. It might have been added afterwards. Thanks for the help!
Forum: Bioinformatics 03-04-2014, 03:26 AM
Replies: 4
Views: 1,321
Posted By albireo
I had the same problem. Would the author of the...

I had the same problem. Would the author of the package be so kind to update the vignette to specify that the package Biobase is required? Thanks a lot!
Forum: Bioinformatics 02-17-2014, 05:33 AM
Replies: 7
Views: 2,256
Posted By albireo
What happens if you try samdump on the same SRA...

What happens if you try samdump on the same SRA files instead?
Forum: Sample Prep / Library Generation 01-27-2014, 07:12 AM
Replies: 20
Views: 9,107
Posted By albireo
The antibody should be sound. We've been ...

The antibody should be sound.

We've been wondering if it is more a case of the exonuclease failing to stop at the crosslinking site, while stopping at various points before. This could be due to...
Forum: Sample Prep / Library Generation 01-27-2014, 05:32 AM
Replies: 20
Views: 9,107
Posted By albireo
Hi, yes that is what I meant. I have performed a...

Hi, yes that is what I meant. I have performed a number of FRiP analyses (similarly to what done in the 2012 ENCODE Genome Research ChIP-seq methods paper) with very disappointing results in one case...
Forum: Sample Prep / Library Generation 01-27-2014, 03:38 AM
Replies: 20
Views: 9,107
Posted By albireo
I have been analysing illumina-based human...

I have been analysing illumina-based human Chip-exo data for a while - in my experience, the results are very TF-dependant.

At best, results (in terms of peak resolution and SN ratio) are almost...
Forum: Bioinformatics 01-24-2014, 06:01 AM
Replies: 2
Views: 1,512
Posted By albireo
Hi, is anyone able to answer the original...

Hi, is anyone able to answer the original question? I would also be interested in using this tool. Unfortunately, the authors have not been very helpful when asked to help.
Forum: Bioinformatics 09-24-2013, 03:02 AM
Replies: 25
Views: 19,014
Posted By albireo
Thanks a lot Alex

Thanks a lot Alex
Forum: Bioinformatics 09-24-2013, 01:41 AM
Replies: 25
Views: 19,014
Posted By albireo
Hi, I'm getting the same error. Has anybody found...

Hi, I'm getting the same error. Has anybody found out the reason of this exception? Thanks!
Forum: Bioinformatics 07-10-2013, 09:24 AM
Replies: 2
Views: 1,012
Posted By albireo
Thanks, I will do that!

Thanks, I will do that!
Forum: Bioinformatics 07-09-2013, 06:11 AM
Replies: 2
Views: 1,012
Posted By albireo
How to upload bigwig tracks to UCSC when a server is not available?

Hi

I need to visualise some bigwig tracks to ucsc.

However uploading them won't work - UCSC wants me to upload them on some personal server and then provide the link in the custom track field....
Forum: Bioinformatics 06-13-2013, 03:19 AM
Replies: 0
Views: 1,647
Posted By albireo
Best place to get .vcf with genotypes for HapMap cell lines?

Hi

I need to obtain SNPs and genotypes for 30 lymphoblastoid cell lines.

I had been told these 30 individuals (CEU and YRI) had all been genotyped as part of the 1000genomes project, however...
Forum: Genomic Resequencing 06-10-2013, 07:36 AM
Replies: 12
Views: 5,398
Posted By albireo
Hi, I have the same problem as the OP. I...

Hi, I have the same problem as the OP. I understand how to slice the chromosome data using VCF tools, however I would be glad if you could explain how to stream the data directly to VCF tools without...
Forum: Bioinformatics 05-21-2013, 04:51 AM
Replies: 3
Views: 1,708
Posted By albireo
works like a charm thanks a lot!!

works like a charm thanks a lot!!
Forum: Bioinformatics 05-20-2013, 02:35 AM
Replies: 3
Views: 1,708
Posted By albireo
Splitting a bed file in multiple bed files by track

Hi

I have a large combined bed files with several tracks (peaks called for several experiments) of the form

track name="track name 1" description="description1" visibility=2...
Forum: Bioinformatics 05-10-2013, 05:06 AM
Replies: 11
Views: 3,991
Posted By albireo
Ok, we agree on that. My original question was:...

Ok, we agree on that. My original question was: how do I get the proportion of lines in the BWA .bam which map only to one location of the genome? It is certainly not the output of your line, because...
Forum: Bioinformatics 05-10-2013, 04:57 AM
Replies: 11
Views: 3,991
Posted By albireo
Thanks, so is the following bamtools output...

Thanks, so is the following bamtools output wrong, or am I misunderstanding something?

Total reads: 2307803
Mapped reads: 2103778 (91.1593%)
Forum: Bioinformatics 05-10-2013, 04:50 AM
Replies: 11
Views: 3,991
Posted By albireo
Hi, thanks for this. I do get 0 with this...

Hi, thanks for this. I do get 0 with this command. However I still don't understand why

samtools view -F 256 your_file.bam | wc -l

gives me the total number of reads, and not the uniquely...
Forum: Bioinformatics 05-10-2013, 03:50 AM
Replies: 11
Views: 3,991
Posted By albireo
Hi thanks, but this is not working. If I use it...

Hi thanks, but this is not working. If I use it with a .bam file obtained with bwa, It just gives me the total number of reads in the .bam, 2307803 (corresponding to the "reads processed" in the...
Forum: Bioinformatics 05-10-2013, 03:26 AM
Replies: 11
Views: 3,991
Posted By albireo
How to count uniquely mapping reads with BWA?

Apologies if this has been asked before.

I'm quite familiar with Bowtie, which I use with the following options:

--best --strata -m 1

To retrieve only "uniquely" mapping chip-seq reads. On...
Forum: Bioinformatics 04-12-2013, 06:44 AM
Replies: 4
Views: 2,334
Posted By albireo
Thanks, looks like bedtools had exactly what I...

Thanks, looks like bedtools had exactly what I was looking for!
Forum: Bioinformatics 04-12-2013, 03:44 AM
Replies: 4
Views: 2,334
Posted By albireo
Count number of reads in peaks?

Hi

I have single-end chip-seq reads mapped to hg19. I have called peaks and have a .bed output.

Is there a software that scans the intervals in the bed and, referencing the .bam alignment,...
Forum: Bioinformatics 04-08-2013, 04:43 AM
Replies: 14
Views: 4,079
Posted By albireo
Hi Rory thanks a lot for the great info.

Hi Rory

thanks a lot for the great info.
Forum: Bioinformatics 04-08-2013, 03:20 AM
Replies: 14
Views: 4,079
Posted By albireo
I agree with your points. My concerns have...

I agree with your points.

My concerns have more to do with tthe idea of doing quantitative chip-seq differential analysis. Even supposing we do have replicates, isn't chip-seq considered...
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