SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 62
Search took 0.02 seconds.
Search: Posts Made By: biocomputer
Forum: Bioinformatics 01-06-2017, 08:39 AM
Replies: 2
Views: 1,597
Posted By biocomputer
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....
Forum: General 12-15-2016, 09:01 AM
Replies: 5
Views: 1,744
Posted By biocomputer
Does including exons and splice sites make the...

Does including exons and splice sites make the alignment more accurate, faster, or both?
Forum: Bioinformatics 12-12-2016, 08:34 AM
Replies: 3
Views: 1,230
Posted By biocomputer
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...
Forum: Bioinformatics 12-09-2016, 01:05 PM
Replies: 3
Views: 1,230
Posted By biocomputer
HISAT2 and different Illumina versions/Phred quality scores

I have some RNA-seq data and FastQC says some of the files have quality scores encoded with "Illumina 1.5" and some with "Sanger / Illumina 1.9". HISAT2 has the option to specify --phred33 or...
Forum: Bioinformatics 04-20-2016, 04:41 PM
Replies: 0
Views: 773
Posted By biocomputer
Question Stats help, interpreting the output of bedtools fisher

Forgive me if this is trivial, I want to make sure I understand the output of bedtools fisher. I've used it to compare several sets of intervals in the human genome and want to say whether two sets...
Forum: Bioinformatics 03-15-2016, 11:23 AM
Replies: 4
Views: 868
Posted By biocomputer
Ah those are warnings not errors, I corrected the...

Ah those are warnings not errors, I corrected the original post.

Here's the output from #3:

https://dl.dropboxusercontent.com/u/8162364/bedtools%20%28g%2B%2B%20gcc%205.3.0%29.txt
Forum: Bioinformatics 03-15-2016, 11:12 AM
Replies: 4
Views: 868
Posted By biocomputer
Question 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...
Forum: Bioinformatics 02-08-2016, 10:01 AM
Replies: 641
Views: 136,455
Posted By biocomputer
I'm using 0.14.4:

I'm using 0.14.4:
Forum: Bioinformatics 01-31-2016, 06:51 PM
Replies: 641
Views: 136,455
Posted By biocomputer
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,...
Forum: Bioinformatics 01-18-2016, 01:07 PM
Replies: 1
Views: 529
Posted By biocomputer
What kind of experiments are they? Biological or...

What kind of experiments are they? Biological or technical replicates? For example, if it's RNA-seq you want to keep your biological replicates separate so you can provide replicates to the program...
Forum: Bioinformatics 11-18-2015, 04:55 PM
Replies: 2
Views: 628
Posted By biocomputer
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...
Forum: Bioinformatics 08-30-2015, 10:04 PM
Replies: 1
Views: 471
Posted By biocomputer
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...
Forum: Bioinformatics 08-18-2015, 11:09 AM
Replies: 3
Views: 826
Posted By biocomputer
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...
Forum: Bioinformatics 08-14-2015, 10:51 AM
Replies: 3
Views: 826
Posted By biocomputer
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...
Forum: Bioinformatics 07-25-2015, 03:14 AM
Replies: 1
Views: 751
Posted By biocomputer
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...
Forum: RNA Sequencing 01-21-2015, 11:45 AM
Replies: 13
Views: 4,798
Posted By biocomputer
I was able to solve my problem. Despite the "-b...

I was able to solve my problem. Despite the "-b genome.fa" seemingly being the cause of the problem it's actually the .gtf file. See here how to modify the .gtf file:
...
Forum: RNA Sequencing 01-12-2015, 01:12 PM
Replies: 13
Views: 4,798
Posted By biocomputer
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...
Forum: Bioinformatics 01-07-2015, 06:05 PM
Replies: 5
Views: 2,118
Posted By biocomputer
The patched version is working more than twice as...

The patched version is working more than twice as fast (actually went just a little bit faster but using -p16 instead of -p32), so that's good.

But now I'm having a problem that I've encountered...
Forum: Bioinformatics 01-07-2015, 02:53 PM
Replies: 21
Views: 6,158
Posted By biocomputer
I'm having pretty much the exact same problem. ...

I'm having pretty much the exact same problem. I'm getting a segfualt from all the Tuxedo tools I've tried (cufflinks, cuffdiff, cuffquant), I'm not exceeding memory, they're are few or no mapped...
Forum: Bioinformatics 01-07-2015, 02:39 PM
Replies: 5
Views: 2,118
Posted By biocomputer
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?
Forum: Bioinformatics 01-06-2015, 09:31 AM
Replies: 5
Views: 2,118
Posted By biocomputer
Thank you, yes I definitely plan to try other...

Thank you, yes I definitely plan to try other programs besides cufflinks/Tuxedo to compare results.
Forum: Bioinformatics 01-05-2015, 11:57 PM
Replies: 5
Views: 2,118
Posted By biocomputer
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...
Forum: Bioinformatics 12-18-2014, 01:17 PM
Replies: 0
Views: 723
Posted By biocomputer
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....
Forum: Bioinformatics 12-09-2014, 04:36 PM
Replies: 11
Views: 1,666
Posted By biocomputer
@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...
Forum: Bioinformatics 12-09-2014, 02:20 PM
Replies: 11
Views: 1,666
Posted By biocomputer
The .bam files I received were already aligned I...

The .bam files I received were already aligned I didn't realize an unaligned .bam file is something people use.
Showing results 1 to 25 of 62

 


All times are GMT -8. The time now is 10:15 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO