Forum: Bioinformatics
01-06-2017, 08:39 AM
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Replies: 2
Views: 3,096
NextSeq variable length reads
I've looked at about a hundred RNA- and ChIP-seq samples from HiSeq machines (from our lab, GEO, or ENCODE) over the last few years and within each sample every read length is always the same (ie....
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Forum: General
12-15-2016, 09:01 AM
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Replies: 5
Views: 4,300
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Forum: Bioinformatics
12-12-2016, 08:34 AM
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Replies: 3
Views: 2,395
It's two sets of sequencing from a year or two...
It's two sets of sequencing from a year or two apart all done several years ago but I don't know exactly when, I can try to find out. But the samples from the first (older) batch are all indicated...
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Forum: Bioinformatics
12-09-2016, 01:05 PM
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Replies: 3
Views: 2,395
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Forum: Bioinformatics
04-20-2016, 04:41 PM
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Replies: 0
Views: 2,217
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Forum: Bioinformatics
03-15-2016, 11:23 AM
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Replies: 4
Views: 1,714
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Forum: Bioinformatics
03-15-2016, 11:12 AM
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Replies: 4
Views: 1,714
Installing bedtools, intel vs gcc compiler
I'm installing Bedtools for myself on a HPC cluster, the Bedtools website indicates it uses the GCC compiler while the cluster I'm working on uses the Intel compiler by default and says GCC is not...
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Forum: Bioinformatics
02-08-2016, 10:01 AM
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Replies: 648
Views: 191,036
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Forum: Bioinformatics
01-31-2016, 06:51 PM
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Replies: 648
Views: 191,036
When I try to run bismark2bedGraph from a...
When I try to run bismark2bedGraph from a directory that doesn't directly contain the input file it fails to find the input file, even though I've specified the path to the input file. For example,...
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Forum: Bioinformatics
01-18-2016, 01:07 PM
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Replies: 1
Views: 1,065
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Forum: Bioinformatics
11-18-2015, 04:55 PM
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Replies: 2
Views: 1,219
Bismark CpA dinucleotides
I would like to specifically look at CpA dinucleotide methylation (ie. make a bedgraph) like I can with CpG's using Bismark. What is the best way to do this? I think I could run bedGraph2cytosine...
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Forum: Bioinformatics
08-30-2015, 10:04 PM
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Replies: 1
Views: 1,094
Is this bisulfite sequencing stranded or not?
This is my first time analyzing bisulfite sequencing. I've downloaded this ENCODE whole genome bisulfite sequencing (http://www.encodeproject.org/experiments/ENCSR020GGM/) data to analyze using...
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Forum: Bioinformatics
08-18-2015, 11:09 AM
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Replies: 3
Views: 1,589
Cool I didn't know about that. I'm actually...
Cool I didn't know about that. I'm actually using bedtools in an Ubuntu VM under Windows but was working in a shared folder so it was trying to to untar and create the aux folders on a Windows...
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Forum: Bioinformatics
08-14-2015, 10:51 AM
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Replies: 3
Views: 1,589
Bedtools 2.24.0 errors while decompressing .tar
When I decompress bedtools 2.24.0:
tar -zxvf ./bedtools-2.24.0.tar.gz
I get several errors:
tar: bedtools2/src/utils/aux: Cannot mkdir: Protocol error
tar: bedtools2/src/utils/aux: Cannot...
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Forum: Bioinformatics
07-25-2015, 03:14 AM
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Replies: 1
Views: 1,357
This is an old question but I'll reply here...
This is an old question but I'll reply here instead of making a new post. There's another old unanswered question asking basically the same thing, and also mentions choosing regions with respect to...
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Forum: RNA Sequencing
01-21-2015, 11:45 AM
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Replies: 13
Views: 7,826
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Forum: RNA Sequencing
01-12-2015, 01:12 PM
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Replies: 13
Views: 7,826
I'm using Cufflinks 2.2.1 and having the same...
I'm using Cufflinks 2.2.1 and having the same problem with cufflinks and cuffdiff. -b causes a segfault, it works fine without it. I ensured the genome.fa and gtf file have their chromosomes in the...
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Forum: Bioinformatics
01-07-2015, 06:05 PM
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Replies: 5
Views: 2,932
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Forum: Bioinformatics
01-07-2015, 02:53 PM
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Replies: 21
Views: 8,143
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Forum: Bioinformatics
01-07-2015, 02:39 PM
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Replies: 5
Views: 2,932
Actually I just came across this and I'm...
Actually I just came across this and I'm currently trying it, if that is the cause of my problem do you know if I should expect a large or small speed improvement using this patch?
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Forum: Bioinformatics
01-06-2015, 09:31 AM
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Replies: 5
Views: 2,932
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Forum: Bioinformatics
01-05-2015, 11:57 PM
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Replies: 5
Views: 2,932
Cufflinks runtime
Cufflinks 2.2.1 is taking a really long time. I start with 45 million 100bp paired-end, rRNA depleted, stranded reads aligned with STAR, 24 million uniquely align, 15 million are multimappers, using...
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Forum: Bioinformatics
12-18-2014, 01:17 PM
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Replies: 0
Views: 1,200
ChIP/RNA-seq replicates
We are setting up a series of ChIP-seq and RNA-seq experiments from a few different cell lines with control and experimental samples for each. The following refers to biological replicates:
1....
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Forum: Bioinformatics
12-09-2014, 04:36 PM
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Replies: 11
Views: 3,584
@blancha
I see you're in Montreal, and we've...
@blancha
I see you're in Montreal, and we've been using Genome Quebec and they are providing BWA-aligned .bam files similar to what you've described, same facility?
@GenoMax
If blancha and I...
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Forum: Bioinformatics
12-09-2014, 02:20 PM
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Replies: 11
Views: 3,584
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