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Forum: Illumina/Solexa 08-24-2015, 04:47 AM
Replies: 6
Views: 6,631
Posted By geneart
Hi all, on the other end , using NEBNext high...

Hi all, on the other end , using NEBNext high fidelity kit I had libraries made. Used 1% phiX. But miSeq failed giving an error saying "clutering failed". There is absolutely nothing to see why or...
Forum: Bioinformatics 06-05-2014, 07:48 AM
Replies: 8
Views: 3,473
Posted By geneart
Ok thanks very much for all your advice and help...

Ok thanks very much for all your advice and help ! Appreciate it !
geneart.
Forum: Bioinformatics 06-05-2014, 07:36 AM
Replies: 8
Views: 3,473
Posted By geneart
Ok. I just checked . They are exactly the same. ...

Ok. I just checked . They are exactly the same.
> res.cds <- exactTest(cds, dispersion="common")
> res.cds
An object of class "DGEExact"
$table
logFC logCPM PValue...
Forum: Bioinformatics 06-05-2014, 07:21 AM
Replies: 8
Views: 3,473
Posted By geneart
dpryan from BioStars reply

Sorry dpryan, my posting limit exceeded on BioStars. hence posting on seqanswers. Pertaining to your previous comment on BioStars here is what Idid:
Yes I checked it again:

>...
Forum: Bioinformatics 06-05-2014, 05:37 AM
Replies: 8
Views: 3,473
Posted By geneart
dpryan ......you are correct :) I did post it...

dpryan ......you are correct :)
I did post it on BioStars as well. Here is the same reply :)

>group <- c(rep("Control", 7), rep("Infected", 8))

> cds <- DGEList( counts , group = group )

>...
Forum: Bioinformatics 06-05-2014, 04:04 AM
Replies: 8
Views: 3,473
Posted By geneart
EdgeR question

Hi all,

I was using EdgeR to perform a DE analysis and following the document http://cgrlucb.wikispaces.com/file/view/edgeR_Tutorial.pdf/258271808/edgeR_Tutorial.pdf.

Essentially edgeR...
Forum: Bioinformatics 05-28-2014, 10:06 AM
Replies: 0
Views: 850
Posted By geneart
HTSeq-genomic array v/s Bedtools intervals

Hello all,
I was playing with bedtools intervals to create a genomic interval of my NGS reads and trying to assess the depth of my reads at each interval, so I can create my own GTF file based on...
Forum: Bioinformatics 05-23-2014, 09:28 AM
Replies: 4
Views: 2,631
Posted By geneart
EdgeR

Thanks Gordon, the tagwise dispersion actually worked. :)
Forum: Bioinformatics 05-14-2014, 10:47 AM
Replies: 4
Views: 2,631
Posted By geneart
Thanks for the email Gordon, I actually did...

Thanks for the email Gordon,
I actually did that wihtout a prior.n value and it there was no error. However I am not sure if it did use the default value for prior.n. Infact it might not have used...
Forum: Bioinformatics 05-09-2014, 10:24 AM
Replies: 4
Views: 2,631
Posted By geneart
EdgeR Vs DESeq2 question

Hello Folks,
I am analysing a dataset using edgeR and DESEq2 and trying to understand what I am seeing.
Here is what I have so far:
I do not have any technical replicates of my samples,...
Forum: Bioinformatics 04-20-2014, 02:51 AM
Replies: 26
Views: 10,949
Posted By geneart
dpryan: you are correct. By Non unique I meant...

dpryan: you are correct. By Non unique I meant not the reads as non unique but the mapping location of reads as non unique. So in essence what I meant is I kept reads mapping to unique location...
Forum: Bioinformatics 04-19-2014, 09:54 AM
Replies: 26
Views: 10,949
Posted By geneart
Mapping uniquely

Hi I have a very basic question about read mapping. For differential expression analysis of NGS data , many papers I have read , mention that they discard non -unique mapping reads. However I could...
Forum: Bioinformatics 04-14-2014, 06:29 PM
Replies: 28
Views: 10,381
Posted By geneart
Thanks Mike for the input. Appreciate it very...

Thanks Mike for the input. Appreciate it very much !
geneart.
Forum: Bioinformatics 04-14-2014, 03:34 AM
Replies: 28
Views: 10,381
Posted By geneart
Update on mike's tip on plotMA, it worked ! i...

Update on mike's tip on plotMA, it worked ! i used ;
DESeq:: plotMA(res)
or DESeq2:: plotMA(your requirements)

I have another question. I am working with 4 animals as my samples with absolutely...
Forum: Bioinformatics 03-26-2014, 02:06 PM
Replies: 28
Views: 10,381
Posted By geneart
DESeq2 plotMA()

Thanks very much Mike !
Will definitely try out what you said and will update soon :)
Regards
geneart.
Forum: Bioinformatics 03-26-2014, 09:27 AM
Replies: 28
Views: 10,381
Posted By geneart
Hello all, This seems to be my problem as well...

Hello all,
This seems to be my problem as well ! I have tried plotMA on DESeq and DESeq2 but I get this same error as mentioned by cacti: Here is my session info . hopefully there is something...
Forum: RNA Sequencing 03-14-2014, 09:08 AM
Replies: 192
Views: 54,721
Posted By geneart
DESeq analysis using HTSeq count data: Problems ...

DESeq analysis using HTSeq count data: Problems
Im following the DESeq guide to perform a differential expression analysis on my HTSeq count data across 7 samples together, without biological...
Forum: RNA Sequencing 03-13-2014, 08:22 AM
Replies: 192
Views: 54,721
Posted By geneart
Hi all, I am working with DESeq and got to the...

Hi all,
I am working with DESeq and got to the point of calling nbinom. However I am getting this error and could not see why?
Just a primer on my work: I have 7 samples which have no replicates. ...
Forum: Bioinformatics 02-26-2014, 11:04 AM
Replies: 10
Views: 27,362
Posted By geneart
Thanks very much!! Will rerun the process with...

Thanks very much!! Will rerun the process with new version.
Forum: Bioinformatics 02-26-2014, 09:47 AM
Replies: 10
Views: 27,362
Posted By geneart
Hello Folks, I had a question about HTSeq...

Hello Folks,
I had a question about HTSeq output which is kind of in tune with this blog....I have sam files as output as well as the count data in text format. So I wanted to look at the no_feature...
Forum: Bioinformatics 11-22-2013, 10:00 AM
Replies: 7
Views: 3,624
Posted By geneart
Smile Rfam blastn search

Hello all,
I am trying to analyze miRNA data and am at a point to clear off all "junk" sequences from my data. In order to do that I used Rfam fasta files, locally installed as a database but...
Forum: General 10-31-2013, 08:28 AM
Replies: 11
Views: 15,695
Posted By geneart
Hello all, I have a similar related question to...

Hello all,
I have a similar related question to extract chromosome positions and depth per region. So I used bedtools to get bam to bed conversion:
I got :
Chr1 11419 11425 HWUSI-# 1 ...
Forum: Bioinformatics 07-27-2013, 01:33 PM
Replies: 2
Views: 1,138
Posted By geneart
Thanks very much ! much appreciated, geneart

Thanks very much ! much appreciated,
geneart
Forum: Bioinformatics 07-25-2013, 11:54 AM
Replies: 2
Views: 1,138
Posted By geneart
Cuffdiff analysis with multiple files

Hello All,
I am trying out cuffdiff and cummeRbund currently and learnt that multiple files can be run to analyse expression. My understanding is that multiple (different samples) can be uploaded to...
Forum: Bioinformatics 07-01-2013, 12:42 PM
Replies: 6
Views: 4,656
Posted By geneart
Hi all, I had a few questions about cufflinks...

Hi all,
I had a few questions about cufflinks for RNA seq analysis.
first : I understand cufflinks is designed for RNA seq and not specifically for miRNA seq.
I am working with miRNA data from...
Showing results 1 to 25 of 42

 


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