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Search: Posts Made By: enelkinsan
Forum: Bioinformatics 07-19-2015, 10:09 AM
Replies: 1
Views: 1,519
Posted By enelkinsan
This loos like input problem. Check if your fastq...

This loos like input problem. Check if your fastq files for 3 fails are in correct format.
Forum: Bioinformatics 08-29-2014, 10:41 PM
Replies: 7
Views: 3,320
Posted By enelkinsan
That's all right, but how the number of mapped...

That's all right, but how the number of mapped reads (bowtie2, accepted_hits.bam) can be bigger than number of reads in the original fastq file? I got this result once and I'm slightly confused how...
Forum: Bioinformatics 06-05-2013, 08:38 PM
Replies: 1
Views: 1,152
Posted By enelkinsan
DESeq on "small genome" data

Hi guys,
I'm interested in your opinion, whether it is a good idea to use DESeq application for DE in an experiment where number of transcripts present in the sequencing mixture would be extremely...
Forum: Bioinformatics 03-12-2013, 01:28 PM
Replies: 13
Views: 12,645
Posted By enelkinsan
I run cufflinks several times on the linux server...

I run cufflinks several times on the linux server (cufflinks v2.0.2, don't know about the server). One of these runs ended with the same error you have, the others were ok. Neither configuration, nor...
Forum: Bioinformatics 02-18-2013, 04:03 PM
Replies: 5
Views: 5,038
Posted By enelkinsan
yes, I've double-checked the indexes path, it is...

yes, I've double-checked the indexes path, it is correct
later, I managed to run tophat by choosing bowtie1 option (I think, this one may be versions conflict OR... I don't know. My data is not...
Forum: Bioinformatics 02-17-2013, 02:02 PM
Replies: 5
Views: 5,038
Posted By enelkinsan
Hi Jetse, what did you do to your bowtie index...

Hi Jetse,
what did you do to your bowtie index files to solve it? I'm trying to run tophat on the pre-build indexes from the cufflinks page and keep getting the same error


tophat...
Forum: Bioinformatics 01-03-2013, 01:25 PM
Replies: 2
Views: 1,580
Posted By enelkinsan
custom reference genome for RNA-seq

Dear all,
I have RNA-seq data with 20 target genes and 5 reference genes (human). I don't want to map it to the whole genome because I'm only interested in those 25.
Probably, there is a way to...
Forum: Bioinformatics 12-18-2012, 02:09 PM
Replies: 1
Views: 1,344
Posted By enelkinsan
Update: the problem sort of resolved by using...

Update: the problem sort of resolved by using Tablet instead of IGV
Forum: Bioinformatics 12-18-2012, 01:58 PM
Replies: 1
Views: 1,344
Posted By enelkinsan
IGV reading .bam

Hi all,
I'm trying to open .bam file in IGV but I keep getting "sorted.bam does not contain any sequence names which match the current genome" error.
I'm slightly puzzled were to look, because I've...
Forum: RNA Sequencing 12-18-2012, 12:42 PM
Replies: 7
Views: 2,484
Posted By enelkinsan
Well, I didn't get it either, I just translated...

Well, I didn't get it either, I just translated someone's remark, as he was quoting someone else. If I ever run into that quoted guy, I'd ask him. Meanwhile, we are turning to stranded protocol anyway
Forum: RNA Sequencing 12-10-2012, 12:56 PM
Replies: 7
Views: 2,484
Posted By enelkinsan
Ok, on today's meeting there came a reply to my...

Ok, on today's meeting there came a reply to my question: apparently, non-stranded protocol is preferable if transcripts are likely to appear on both strands.
In all other cases stranded goes best....
Forum: RNA Sequencing 12-09-2012, 12:02 PM
Replies: 7
Views: 2,484
Posted By enelkinsan
Thanks for that! By the way, it makes me...

Thanks for that!
By the way, it makes me thinking - why would people need non-stranded protocol than? There must be some "pro-s", or it would just die off...
Forum: RNA Sequencing 12-06-2012, 12:54 PM
Replies: 7
Views: 2,484
Posted By enelkinsan
stranded or non-stranded protocol?

Hi, all
we've got a differential expression study on some poorly annotated organism (fish), and the task is to compare expression in different tissues. I was wondering, may be someone has any...
Forum: Bioinformatics 10-29-2012, 03:45 PM
Replies: 11
Views: 8,695
Posted By enelkinsan
bioconductor, some useDevel compatibility?

Hi,
I'm relatively new to the R topic and currently trying ot install Bioconductor (actually, a tutorial material on it). I've got a strange error message and wonder if anybody could help me with...
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