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Search: Posts Made By: ugolino
Forum: Bioinformatics 06-27-2013, 12:31 PM
Replies: 0
Views: 3,898
Posted By ugolino
DESeq: intepreting results from interaction analysis

Hi there,

I am using DESeq to infer differential gene expression in a 2-factor design. Factor 1 (strain) and Factor 2 (condition) each have 4 levels; 3 bioreps each totaling to 48 samples. I am...
Forum: Bioinformatics 11-16-2012, 11:21 AM
Replies: 2
Views: 2,197
Posted By ugolino
Is my post poorly formulated or simply inane? I...

Is my post poorly formulated or simply inane? I wonder why is it being ignored?

thanks
Forum: Bioinformatics 11-15-2012, 11:10 AM
Replies: 2
Views: 2,197
Posted By ugolino
here is the table again DESeq edgeR ...

here is the table again

DESeq edgeR
comparison FDR 5% FC>2 FDR 5% FC>2 overlap
A/B 599 467 896 604 599
A/C 0 0 na
A/D 550 400 879 573 548
B/C 676 523 972 640 676
B/D 0 0 na...
Forum: Bioinformatics 11-15-2012, 11:07 AM
Replies: 2
Views: 2,197
Posted By ugolino
advice on DESeq and EdgeR output from bacterial RNA-seq

Hi there,

I'm analyzing RNA-seq data from a bacterial monoculture exposed to 4 conditions. There are 3 bioreps for each condition and after aligning to reference using bowtie2, getting read...
Forum: Bioinformatics 10-30-2012, 05:09 PM
Replies: 8
Views: 4,963
Posted By ugolino
correction, bed format is 0-based start and...

correction, bed format is 0-based start and 1-based end, so it's the same as htseq.
Forum: Bioinformatics 10-30-2012, 04:30 PM
Replies: 8
Views: 4,963
Posted By ugolino
Hi Proteos, I am also interested in read...

Hi Proteos,

I am also interested in read coverage of intergenic regions and have only bed formatted coordinates for those. Could you possibly share or give instruction on how to modify...
Forum: Bioinformatics 10-19-2012, 11:54 AM
Replies: 14
Views: 25,966
Posted By ugolino
Following your tip I ran a PE RNA-seq alignment...

Following your tip I ran a PE RNA-seq alignment with these options.
bowtie2 --no-contain -a --no-mixed

Then fed SAM output file to htseq-count (w/ -s no option as it's a non-stranded library)...
Forum: Bioinformatics 10-19-2012, 06:30 AM
Replies: 3
Views: 4,395
Posted By ugolino
To align reads with greater confidence, as these...

To align reads with greater confidence, as these strains have many phages and IS elements ( some of which are chromosomal in certain strains and plasmid borne in others ), and their genomes have not...
Forum: Bioinformatics 10-18-2012, 04:09 PM
Replies: 3
Views: 4,395
Posted By ugolino
I think I figured it out. Bowtie2 outputs by...

I think I figured it out. Bowtie2 outputs by default reads sorted by name. The offending part in the reads is the _1, _2 at the end. Removing those (in vim) fixed the problem and htseq-count works...
Forum: Bioinformatics 10-18-2012, 01:49 PM
Replies: 3
Views: 4,395
Posted By ugolino
convert sorted bam to sorted sam for htseq-count

Hi there,

I have a bowtie2 alignment of PE non-stranded RNA-seq reads from a bacterial species (used option -k 1; 96.20% pairs aligned concordantly exactly 1 time) , and would like to use...
Forum: Illumina/Solexa 09-25-2012, 01:41 PM
Replies: 9
Views: 5,944
Posted By ugolino
this is a perl script from velvet's contrib...

this is a perl script from velvet's contrib folder and will do what you need so long as the reads from two separate files are paired.

shuffleSequences_fastq.pl

#!/usr/bin/perl

$filenameA =...
Forum: Illumina/Solexa 09-25-2012, 01:30 PM
Replies: 9
Views: 5,944
Posted By ugolino
I don't understand what use will those reads be...

I don't understand what use will those reads be to you once you merge them? The positional information, ie 90 bp in between, is also critical to the assembly. Why do you want to merge them?
Forum: Bioinformatics 09-25-2012, 01:11 PM
Replies: 4
Views: 3,619
Posted By ugolino
Thanks for the reply! Perhaps I did not...

Thanks for the reply!

Perhaps I did not explain well. The strain that I'm using has a phage that is not present in the complete genomes of closely related strains. Hence mapping to those...
Forum: Bioinformatics 09-25-2012, 10:47 AM
Replies: 4
Views: 3,619
Posted By ugolino
Post bacterial RNA-seq mapping to draft genome

Hi there,

I have DNA and RNA-seq data from pathogenic E. coli, on Illumina GA-IIx, 68 bp PE reads. There is no complete genome for the strains I used. Although several genomes from closely...
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