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Search: Posts Made By: shikha5
Forum: Bioinformatics 01-07-2015, 05:22 AM
Replies: 9
Views: 2,940
Posted By shikha5
Hi @areyes, Thanks for your reply. You have...

Hi @areyes,
Thanks for your reply. You have correctly pointed out that, the error I was getting was due to the "absence of replicates" in the analysis. But, when I included 2 replicates then it was...
Forum: Bioinformatics 12-22-2014, 12:34 AM
Replies: 9
Views: 2,940
Posted By shikha5
Hi All, Now I am considering the replicates too...

Hi All,
Now I am considering the replicates too but getting the same error as mentioned in my last post on this thread.

Can anybody help?
Forum: Bioinformatics 12-17-2014, 12:16 AM
Replies: 9
Views: 2,940
Posted By shikha5
countFiles =...

countFiles = list.files("/dati/data_svashisht/CARIPLO_Project_files/TopHat2_New_alignments_28_11_2014/dexseqCounts", full.names=TRUE)
flattenedFile =...
Forum: Bioinformatics 12-16-2014, 08:33 AM
Replies: 9
Views: 2,940
Posted By shikha5
I have the same error :rolleyes: I suspect...

I have the same error :rolleyes:

I suspect this error may be due to no replicates.

as.data.frame(colData(dxd))
sample condition libType exon sizeFactor
1 control SMA-control...
Forum: Bioinformatics 11-21-2014, 10:01 AM
Replies: 14
Views: 6,716
Posted By shikha5
Thanks Devon for you reply :) Actually I...

Thanks Devon for you reply :)

Actually I have tried same thing on full alignments file and the results were same so in order to understand the error i am doing this for only chr22 aligned reads....
Forum: Bioinformatics 11-21-2014, 04:59 AM
Replies: 14
Views: 6,716
Posted By shikha5
htseq-count: all the counts are 0

Hello Simon

:rolleyes:


Command used is:
I have passed the sorted bam converted into sam using

samtools sort -n <accepted_hits_chr22.bam> <out_sorted>
samtools view <sorted.bam>...
Forum: Bioinformatics 07-17-2013, 08:48 AM
Replies: 8
Views: 1,929
Posted By shikha5
Thanks dear for your reply and suggestion. ...

Thanks dear for your reply and suggestion.

Okay, I also think that this is a good idea to consider the replicates of a sample but if I use the DEXSeq tool then it will only tell me about the...
Forum: Bioinformatics 07-17-2013, 01:01 AM
Replies: 8
Views: 1,929
Posted By shikha5
Comparison between two indvidual tissue samples from RNA seq

Hi Everybody
I have a question regarding the RNA seq data analysis in terms of the differential exon usage by two different tissue samples such as comparison between kidney tissue (RNA seq reads...
Forum: Bioinformatics 07-15-2013, 01:37 AM
Replies: 7
Views: 1,227
Posted By shikha5
What If I want the comparison between two...

What If I want the comparison between two individual tissues then according to you which program/tool can serve the need at this moment??
Forum: Bioinformatics 07-15-2013, 01:31 AM
Replies: 7
Views: 1,227
Posted By shikha5
Thanks Dear Alejandro for replying and giving you...

Thanks Dear Alejandro for replying and giving you valuable suggestion.

Okay in that case I should have two replicates of kidney tissue sample and two for the other one and it will compare between...
Forum: Bioinformatics 07-12-2013, 05:18 AM
Replies: 7
Views: 1,227
Posted By shikha5
This is the code I am using for getting the...

This is the code I am using for getting the ExonCountSet Object:
...
Forum: Bioinformatics 07-12-2013, 05:13 AM
Replies: 7
Views: 1,227
Posted By shikha5
Thanks for the reply dpryan. Yes, I am trying...

Thanks for the reply dpryan.
Yes, I am trying to compare two individual samples from two independent tissues.
Forum: Bioinformatics 07-12-2013, 04:41 AM
Replies: 7
Views: 1,227
Posted By shikha5
DEXSeq related query

Hi
My name is shikha and currently I am working on RNA seq data analysis. I want to compare two different tissue samples eg: one from kidney tissue and another from liver (not replicates of same...
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