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Forum: Bioinformatics 06-27-2013, 05:16 PM
Replies: 0
Views: 1,682
Posted By Aurelien Mazurie
SNP calling in orthologous genes rather than reads

Hi all,
I am familiar with the BWA + SAMTOOLS pipeline and how it can be used to call SNPs by comparing reads against a reference genome. In this case, ploidy, coverage and sequence quality...
Forum: Bioinformatics 09-26-2011, 09:23 AM
Replies: 2
Views: 2,295
Posted By Aurelien Mazurie
I moved on other projects since then, and I can't...

I moved on other projects since then, and I can't remember how I fixed (or dealt with) this error anymore. I know I got the pipeline running on the same machines, so the solution wasn't to add...
Forum: De novo discovery 05-18-2011, 04:58 PM
Replies: 82
Views: 48,139
Posted By Aurelien Mazurie
This is something I am wondering: is there any...

This is something I am wondering: is there any way to come up with an RPKM-like measure of expression level when doing de novo transcriptome assembly? Counting the number of reads per contig (cDNA)...
Forum: De novo discovery 05-17-2011, 10:37 AM
Replies: 82
Views: 48,139
Posted By Aurelien Mazurie
Very interesting thread. I am collecting...

Very interesting thread. I am collecting information about the best strategy to perform de novo transcriptome assembly for a plant for which we have no reference genome. From what I read here it...
Forum: Bioinformatics 03-23-2011, 03:11 PM
Replies: 2
Views: 15,803
Posted By Aurelien Mazurie
cuffdiff: making sense of gene_id, p_id, transcript_id and tss_id

Greetings to Cufflinks users,
I am trying to interpret outputs from cuffcompare and cuffdiff to answer the following questions: is there some alternative splicing going on in an experiment (3 time...
Forum: Bioinformatics 03-21-2011, 03:44 PM
Replies: 12
Views: 6,944
Posted By Aurelien Mazurie
Do you know of a good alternative?

Do you know of a good alternative?
Forum: Bioinformatics 03-02-2011, 04:14 PM
Replies: 2
Views: 2,295
Posted By Aurelien Mazurie
Dreaded (because unresolved) bad_alloc error

Greetings,
I run into a 'std::bad_alloc()' error when processing a 500MB BAM file with cufflinks on a 8BG machine. The exact error message is

. . .
> Processed 17748 loci. ...
Forum: Bioinformatics 03-02-2011, 08:39 AM
Replies: 11
Views: 8,178
Posted By Aurelien Mazurie
I got the same error message with a BAM file of...

I got the same error message with a BAM file of about 500 MB on a 4-CPU machines with 12 GB RAM. It is a 64 bits Linux distribution (kernel 2.6.18); I will try to launch the same cufflink job on my...
Forum: Bioinformatics 03-01-2011, 10:58 AM
Replies: 5
Views: 22,046
Posted By Aurelien Mazurie
I found an answer for question (4):...

I found an answer for question (4): http://seqanswers.com/forums/showthread.php?p=13800#post13800

The suggestion from Cole Trapnell is indeed to pool samples with cuffcompare in step 4, then run...
Forum: Bioinformatics 03-01-2011, 10:46 AM
Replies: 5
Views: 22,046
Posted By Aurelien Mazurie
Thank you for the links; I will definitively look...

Thank you for the links; I will definitively look at them. I never heard about diff-express, and couldn't find anything on Google. Could you give some more details about it?

Aurelien
Forum: Bioinformatics 03-01-2011, 10:41 AM
Replies: 10
Views: 6,007
Posted By Aurelien Mazurie
It works, thanks! For those interested I wrote a...

It works, thanks! For those interested I wrote a Python script to do the job, which is enclosed.

Aurelien
Forum: Bioinformatics 03-01-2011, 08:45 AM
Replies: 10
Views: 6,007
Posted By Aurelien Mazurie
Interesting. I checked my SAM files, and the @SQ...

Interesting. I checked my SAM files, and the @SQ lines only have two colons:

@HD VN:1.0 SO:sorted
@SQ SN:EG:bd_7x3 LN:450
@SQ SN:EG:bd_6x3 LN:450
@SQ SN:EG:bd_36x35 ...
Forum: Bioinformatics 02-28-2011, 10:15 AM
Replies: 5
Views: 22,046
Posted By Aurelien Mazurie
Typical TopHat/Cufflinks pipeline?

Greetings,
I am new to RNA-seq analysis, and am trying to understand the high-order logic of the bowtie/tophat/cufflinks/cuffcompare/cuffdiff pipeline. As far as I understand, a typical run would be...
Forum: Bioinformatics 02-28-2011, 09:03 AM
Replies: 10
Views: 6,007
Posted By Aurelien Mazurie
I had exactly the same problem; sorting the BAM...

I had exactly the same problem; sorting the BAM file didn't help.
Forum: RNA Sequencing 02-24-2011, 10:38 AM
Replies: 5
Views: 5,609
Posted By Aurelien Mazurie
I am learning how to use TopHat, and I do have...

I am learning how to use TopHat, and I do have exactly the same question. Do you happen to know the answer?

Aurelien
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