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Forum: De novo discovery 07-21-2012, 12:49 AM
Replies: 7
Views: 3,738
Posted By waterboy
Hello everyone... I am using ray for assembling...

Hello everyone...
I am using ray for assembling HiSeq2000 109 million PE reads. I have given 12 cores for ranks with 144 gb RAM. Can anyone tel me the estimated time it will take and the steps...
Forum: Bioinformatics 04-23-2012, 12:30 AM
Replies: 13
Views: 5,799
Posted By waterboy
how to merge mulitple scaffold files??

Hello All,
I have two scaffold sequence files obtained from assembly of SOLiD MP and 454 PE paired reads. I would like to build super scaffolds using these two scaffold sequence files with the help...
Forum: 454 Pyrosequencing 08-24-2011, 01:31 AM
Replies: 3
Views: 2,740
Posted By waterboy
Hello, Can any one please tell me how to use...

Hello,
Can any one please tell me how to use Newbler's scaffolder, I have contigs and 454 PE reads for scaffolding.

I tried scaffolding using newbler gsAssembler, but I got the following...
Forum: Bioinformatics 03-29-2011, 12:44 AM
Replies: 15
Views: 2,846
Posted By waterboy
Is this suitable for Solid reads.

Is this suitable for Solid reads.
Forum: Bioinformatics 03-29-2011, 12:11 AM
Replies: 15
Views: 2,846
Posted By waterboy
Thank U Yes, me trying it with related species....

Thank U
Yes, me trying it with related species. What are the necessary filterations required before using miRDeep. Please do reply!!!!
Forum: De novo discovery 03-15-2011, 10:01 PM
Replies: 16
Views: 14,948
Posted By waterboy
The read length is 50bp. yes I trimmed the reads...

The read length is 50bp. yes I trimmed the reads before running velvet and oases.
The kmer length that we prefer is 25-31. Even after doing that only 2806127 reads out of 31405877 filtered reads...
Forum: De novo discovery 03-14-2011, 10:10 PM
Replies: 16
Views: 14,948
Posted By waterboy
Hello, I am doing transcriptome de novo...

Hello,
I am doing transcriptome de novo assembly on SOLiD data, for that I am running velvet and oases pipeline, in the assembly outoff 31 million reads only 1 million reads taking part in...
Forum: Bioinformatics 11-22-2010, 08:29 PM
Replies: 5
Views: 1,495
Posted By waterboy
what kind of reads do you have? is it...

what kind of reads do you have? is it transcriptome data or genomic data?
Forum: Bioinformatics 11-22-2010, 08:26 PM
Replies: 2
Views: 1,354
Posted By waterboy
The latest version of cufflinks directly accepts...

The latest version of cufflinks directly accepts the bam file produced by TopHat. you do not need to conver the bam file into sam file. I just did this a couple of days ago.

$./cufflinks -G...
Forum: Bioinformatics 11-21-2010, 10:33 PM
Replies: 1
Views: 2,604
Posted By waterboy
help with differential gene expression with cufflinks and tophat

Hi All,
We are looking for differential gene expression of two different samples of the same species.

After running tophat, for two different samples of the same species, we got accepted_hits.bam...
Forum: Bioinformatics 11-15-2010, 11:01 PM
Replies: 1
Views: 2,802
Posted By waterboy
TOPHAT EMPTY accepted_hits.bam ISSUE

Folks..!

I've been running tophat since a couple of weeks and I've seen no success so far :(
I have colorspace transcriptome data having 97 million reads. I've built Bowtie colorspace index as...
Forum: Bioinformatics 10-29-2010, 07:33 AM
Replies: 4
Views: 1,869
Posted By waterboy
Dear Folks..! Eventually I came to know that...

Dear Folks..!

Eventually I came to know that I downloaded the wrong version myself, and everything works fine now.. :) I've got results on my test data too :) and now I've started my transcriptome...
Forum: SOLiD 10-29-2010, 04:29 AM
Replies: 5
Views: 4,683
Posted By waterboy
Hello Pejmen, I am Shilp Purohit, and I am...

Hello Pejmen,

I am Shilp Purohit, and I am currently working with ABI SOLiD 3 plus sequencer. I am trying to install TopHat 1.1.2 (BETA) on my local machine. The "Getting started" manual suggests...
Forum: Bioinformatics 10-29-2010, 04:20 AM
Replies: 4
Views: 1,869
Posted By waterboy
Red face TopHat Installation problem version 1.1.2

Dear Friends,

I am Shilp Purohit, and I am currently working with ABI SOLiD 3 plus sequencer. I am trying to install TopHat 1.1.2 (BETA) on my local machine. The "Getting started" manual suggests...
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