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Forum: RNA Sequencing 08-08-2016, 08:47 AM
Replies: 0
Views: 967
Posted By mallela
what are the concerns when read length is longer than the reference ?

Hi,

I'm dealing with the expression data of shRNA where the reference sequence (antisense sequence) is about 22bp and the length of the reads produced by ion proton average at 125bp. This is the...
Forum: Bioinformatics 05-10-2016, 08:31 AM
Replies: 18
Views: 4,524
Posted By mallela
Btw, can you paste me your recent cuffdiff...

Btw, can you paste me your recent cuffdiff command that you have used after you have marked the duplicates? Did you use the *_md.bam files?

Why don't you try using cuffquant on your *_md.bam files...
Forum: Bioinformatics 05-10-2016, 05:45 AM
Replies: 18
Views: 4,524
Posted By mallela
how about you try inserting this extra option...

how about you try inserting this extra option into your picard command ? :rolleyes:
REMOVE_DUPLICATES=true
Forum: Bioinformatics 05-09-2016, 10:14 AM
Replies: 18
Views: 4,524
Posted By mallela
These are your read names. If one has to write a...

These are your read names. If one has to write a regex pattern to match such names, it would be this:

"([A-Z0-9]+):([0-9]+):([A-Z0-9]+):([0-9]+):([0-9]+):([0-9]+):([0-9]+)"

Your picard command...
Forum: Bioinformatics 05-09-2016, 08:11 AM
Replies: 18
Views: 4,524
Posted By mallela
can you paste me the output of the following...

can you paste me the output of the following command ? I will then have a better understanding of what you mean.

samtools view accepted_hits.bam | head | cut -f1
Forum: Bioinformatics 05-09-2016, 07:37 AM
Replies: 18
Views: 4,524
Posted By mallela
Forget about the "optical/sequence" terminology....

Forget about the "optical/sequence" terminology. I was just being a little descriptive.
Just read the description on the site for MarkDuplicates and tailor your command according to the read names...
Forum: Bioinformatics 05-09-2016, 07:15 AM
Replies: 18
Views: 4,524
Posted By mallela
The cuffdiff being stuck at 99% is probably...

The cuffdiff being stuck at 99% is probably because of the duplicates in the bam file. When I marked the optical duplicates / sequence duplicates using the picard tools and then input the resultant...
Forum: RNA Sequencing 03-05-2015, 09:51 AM
Replies: 2
Views: 1,612
Posted By mallela
Thanks! That has cleared up some things for me.

Thanks! That has cleared up some things for me.
Forum: RNA Sequencing 03-05-2015, 08:47 AM
Replies: 2
Views: 1,612
Posted By mallela
What is meant by the term "Library" in the context of wet lab & flow cell ?

Hi,

I was reading this (http://dx.doi.org/10.1093/bib/bbs046) paper and I came across the text,

"Because the most obvious source of variation between lanes is the differences in library size...
Forum: Bioinformatics 03-17-2014, 05:47 AM
Replies: 18
Views: 4,524
Posted By mallela
Well, according to the post in cufflinks[1], I...

Well, according to the post in cufflinks[1], I tried masking (-M option) all the repeat regions with the rmsk table obtained from the UCSC & combined with the chrM from the mRNA table of UCSC . But...
Forum: Bioinformatics 03-15-2014, 06:45 AM
Replies: 18
Views: 4,524
Posted By mallela
Hi Devon, Thanks for the hint, I've checked...

Hi Devon,

Thanks for the hint, I've checked my syslogs but I didn't find anything related to the crash. In anycase, I am running on a system with 24 cores and 128GB RAM. When I encountered this...
Forum: Bioinformatics 03-15-2014, 02:20 AM
Replies: 18
Views: 4,524
Posted By mallela
Hi Starr, Did you get to solve the issue. I...

Hi Starr,

Did you get to solve the issue. I am also encountering the same problem.
The system is killing the process at 99% exactly at the location that you mentioned.

Testing for differential...
Forum: Bioinformatics 03-15-2014, 02:12 AM
Replies: 2
Views: 2,540
Posted By mallela
Hi hlwright, I am also having the same...

Hi hlwright,

I am also having the same problem. Could you pls tell me how you've solved your problem ?

Thanks!
Forum: Bioinformatics 05-21-2013, 06:01 AM
Replies: 11
Views: 4,330
Posted By mallela
Very nice Mattia :) My post above is also about...

Very nice Mattia :) My post above is also about "unsetting" -p parameter.

Your solution unsets the -p parameter for all the steps of TopHat right from the beggining, thereby proving no...
Forum: Bioinformatics 05-21-2013, 01:46 AM
Replies: 11
Views: 4,330
Posted By mallela
Wink A 'maybe' Solution

I've solved this problem for now.

Well, I have the same problem. I am dealing with ~170M colorspace reads.

My Tophat Version:
TopHat v2.0.8b

My ERROR:
[2013-05-21 10:55:08] Searching for...
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