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Search: Posts Made By: uqfgaiti
Forum: Bioinformatics 02-27-2014, 11:02 PM
Replies: 15
Views: 3,844
Posted By uqfgaiti
Hi Simon, that's the way I was thinking too....

Hi Simon,

that's the way I was thinking too.

It's nice to hear this from you. I'm not too off

Thanks again for help
Federico
Forum: Bioinformatics 02-27-2014, 02:26 PM
Replies: 15
Views: 3,844
Posted By uqfgaiti
Hi Simon, sorry for that. I'm still a...

Hi Simon,

sorry for that. I'm still a beginner in this field and i'm still learning how all this works.
The thread on bioconductor list is more focused on DESeq2 analysis than htseq-count but I...
Forum: Bioinformatics 02-27-2014, 04:19 AM
Replies: 15
Views: 3,844
Posted By uqfgaiti
Hi Simon, I might have figured this out. ...

Hi Simon,

I might have figured this out.

I think the issue is that I have particular loci in the genome that have overlapping genes on the same strand. Though, these genes have a different ID...
Forum: Bioinformatics 02-27-2014, 03:16 AM
Replies: 15
Views: 3,844
Posted By uqfgaiti
Ok, thanks again for help! Let you know how...

Ok, thanks again for help!

Let you know how it goes
Forum: Bioinformatics 02-27-2014, 02:02 AM
Replies: 15
Views: 3,844
Posted By uqfgaiti
yes my gtf file contains all exon lines for...

yes my gtf file contains all exon lines for antisense transcripts as well.
this explains the discrepancy since I used -s yes for the stranded libraries.
But why sometimes the counts are zero when...
Forum: Bioinformatics 02-26-2014, 05:30 PM
Replies: 15
Views: 3,844
Posted By uqfgaiti
Hi Simon, I have had a look at the...

Hi Simon,

I have had a look at the alignments.
When the counts between stranded and unstraded librarires agree reasonably well, it looks alright. I can see that when they differ strongly it is...
Forum: Bioinformatics 02-26-2014, 12:24 AM
Replies: 15
Views: 3,844
Posted By uqfgaiti
Hi Simon, Good idea! I am sorting my bam...

Hi Simon,

Good idea!
I am sorting my bam files at the moment. I will write back once I had a look at the alignment

In the meantime thanks for the suggestion
Forum: Bioinformatics 02-25-2014, 04:46 AM
Replies: 15
Views: 3,844
Posted By uqfgaiti
Hi Blanco, to be sure I did a quick test...

Hi Blanco,

to be sure I did a quick test using infer_experiment.py,it is indeed forward-reverse. I also did a blat to the genome and I got the same result.



Based on this I ran TOPHAT with...
Forum: Bioinformatics 02-22-2014, 09:36 PM
Replies: 15
Views: 3,844
Posted By uqfgaiti
Low number of replicates DESeq

Hi all,

I am using DESeq for DGE analysis.

I have STRANDED RNA-Seq data for 4 developmental stages with no replicates.
To have a more reliable DGE I should have replicates and so I obtained...
Forum: Bioinformatics 07-12-2013, 10:20 PM
Replies: 1
Views: 2,455
Posted By uqfgaiti
Gene Set Enrichment Analysis

Hi all,

I have used the cummeRbund function findSimilar() to find the 10 most similar genes to the differentially expressed genes I identified using Cuffdiff. This used the Jensen-Shannon distance...
Forum: Bioinformatics 06-29-2013, 03:35 AM
Replies: 0
Views: 1,610
Posted By uqfgaiti
cummeRbund creating gene set

Hi all,

I am using cummeRbund, an R visualization package for Cufflinks high-throughput sequencing data.

I want to create a gene sets to be able to analyse the differentially expressed genes...
Forum: Bioinformatics 04-14-2013, 05:20 PM
Replies: 3
Views: 1,400
Posted By uqfgaiti
print first occurence of a line

Hi all,

I extracted ORFs from a initial fasta file and now I want to get the longest ORF for each transcript.

After having extracted the size of the ORFs with faSize and sorted them by size,...
Forum: Bioinformatics 02-19-2013, 11:33 PM
Replies: 7
Views: 3,397
Posted By uqfgaiti
Hi all, as kove and sschavan above, I was...

Hi all,

as kove and sschavan above, I was running RNA-SeQC software in command line. I tried withto follow the example sets provided on https://confluence.broadinstitute.or...Tools/RNA-SeQC and...
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