Forum: RNA Sequencing
01-28-2015, 07:49 AM
|
|
Replies: 0
Views: 2,003
|
|
Forum: Bioinformatics
06-10-2013, 11:28 AM
|
|
Replies: 648
Views: 190,798
Solved: alignment on one strand only
Just a quick message to let users know that my problem is solved and was due to an error when generating the Bowtie index files for one of the strands. All index files were present, but one of them...
|
|
Forum: Bioinformatics
06-08-2013, 08:27 PM
|
|
Replies: 648
Views: 190,798
Hi Felix
Actually I was running bismark on a...
Hi Felix
Actually I was running bismark on a cluster and I requested 32g of memory. I have now run it with 48g and I'm still encountering the same issue...
Do you have any idea of what else could...
|
|
Forum: Bioinformatics
06-08-2013, 07:17 AM
|
|
Replies: 648
Views: 190,798
Thanks Felix for your answer.
I am now...
Thanks Felix for your answer.
I am now facing another problem: when I run bismark of some of my samples, reads end up mapped to only the top or the bottom strand... This is not happening for all...
|
|
Forum: Bioinformatics
05-30-2013, 11:47 AM
|
|
Replies: 648
Views: 190,798
Dear Felix,
I am wondering if Bismark can be...
Dear Felix,
I am wondering if Bismark can be fed with an input stream in a pipeline.
For example would that work?
cutadapt -b ACTGCTCG input_file.fastq | bismark -n 1 --solexa1.3-quals --bam...
|
|
Forum: Bioinformatics
05-17-2013, 09:22 AM
|
|
Replies: 38
Views: 27,438
|
|
Forum: Bioinformatics
04-12-2013, 01:07 PM
|
|
Replies: 5
Views: 5,759
|
|
Forum: Bioinformatics
04-10-2013, 02:26 PM
|
|
Replies: 5
Views: 5,759
|
|
Forum: RNA Sequencing
03-26-2013, 08:32 AM
|
|
Replies: 1
Views: 3,690
|
|
Forum: Bioinformatics
01-22-2013, 08:28 AM
|
|
Replies: 3
Views: 1,839
|
|
Forum: Bioinformatics
01-08-2013, 02:03 PM
|
|
Replies: 3
Views: 1,839
DEXSeq memory requirements
Dear all,
I am analyzing a RNA-seq experiment with DEXSeq. There are 73 samples (from 23 different conditions).
When trying to estimate the dispersions for the whole exonCountSet (all conditions...
|
|
Forum: Bioinformatics
11-27-2012, 01:30 PM
|
|
Replies: 3
Views: 3,040
Hi Simon,
Thanks for your answer. However I am...
Hi Simon,
Thanks for your answer. However I am not fully convinced that it is not an issue...
In my dataset at least 40% of the reads overlap an exon junction. If you count these read twice when...
|
|
Forum: Bioinformatics
11-15-2012, 03:19 PM
|
|
Replies: 3
Views: 3,040
DEXSeq gene level counts
Dear DEXSeq authors,
I have a question related to the following paragraph in the DEXSeq vignette:
I am wondering if this problem is also affecting the tests for differential expression of exons...
|
|
Forum: Illumina/Solexa
07-19-2012, 10:11 AM
|
|
Replies: 7
Views: 3,176
Mmmm, I'm getting confused...
Now I understand...
Mmmm, I'm getting confused...
Now I understand you don't agree with Simon and what was discussed here: https://mailman.stat.ethz.ch/pipermail/bioconductor/2012-March/044094.html
(Basically, it is...
|
|
Forum: Illumina/Solexa
07-19-2012, 08:07 AM
|
|
Replies: 7
Views: 3,176
Thanks again Alejandro,
If I understood...
Thanks again Alejandro,
If I understood correctly, you suggest to:
- estimate the dispersions on the whole ecs using "estimateDispersions"
- fit the coefficients of the dispersion function from...
|
|
Forum: Illumina/Solexa
07-13-2012, 09:57 AM
|
|
Replies: 7
Views: 3,176
Thanks Alejandro,
Yes indeed, that's what I...
Thanks Alejandro,
Yes indeed, that's what I ended up doing:
> allExonsPairwise <- newExonCountSet(countData = counts(allExons)[, -c(1:3)], design = design(allExons)[-c(1:3),], geneIDs =...
|
|
Forum: Illumina/Solexa
07-12-2012, 08:49 AM
|
|
Replies: 7
Views: 3,176
Pairwise comparisons in DEXSeq
Dear all,
I am analyzing a RNA-seq experiment including more than 2 conditions. As discussed in this topic, I have created a global exonCountSet, including all conditions and their replicates, to...
|
|
Forum: Bioinformatics
04-12-2012, 09:01 AM
|
|
Replies: 4
Views: 3,185
|
|
Forum: Bioinformatics
04-11-2012, 07:59 AM
|
|
Replies: 4
Views: 3,185
|
|
Forum: Bioinformatics
04-10-2012, 10:02 AM
|
|
Replies: 4
Views: 3,185
Tophat 1.4.1 in -G mode
Dear all,
I am trying to map reads from an Illumina RNA-seq run to the human genome.
I am using the command:
~/bin/tophat-1.4.1.Linux_x86_64/tophat --solexa1.3-quals --library-type fr-unstranded...
|
|
Forum: RNA Sequencing
04-06-2012, 07:35 AM
|
|
Replies: 6
Views: 4,543
Probably this is part of the problem since by...
Probably this is part of the problem since by default Tophat only allows 2 mismatches on the whole read. I had a similar problem when analyzing reads of 107bp. Switching to --bowtie-n mode might help...
|
|
Forum: Illumina/Solexa
02-16-2012, 08:27 AM
|
|
Replies: 5
Views: 5,770
Actually not. Some high concentration libraries...
Actually not. Some high concentration libraries also show a noisy peak, while some low concentration libraries look perfectly fine.
Did you sequence the low concentration libraries you're mentioning?
|
|
Forum: Illumina/Solexa
02-15-2012, 01:38 PM
|
|
Replies: 5
Views: 5,770
NextGenSeq: Yes, the DNA is fragmented before...
NextGenSeq: Yes, the DNA is fragmented before cDNA synthesis, with the Elute, Prime, Fragment Mix (EPF) provided by Illumina. I'm not sure the problem comes from this step since other libraries of...
|
|
Forum: Illumina/Solexa
02-15-2012, 11:02 AM
|
|
Replies: 5
Views: 5,770
weird noisy peaks on bioanalyzer
Hi everyone,
We are getting some weird results when running RNA-seq libraries on Agilent Bioanalyzer.
The libraries show a peak at the expected length, but the peak itself is very noisy, with a...
|
