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Forum: Bioinformatics 02-25-2013, 06:48 PM
Replies: 1
Views: 766
Posted By vinay052003
Computing time of TopHat can be improved by first...

Computing time of TopHat can be improved by first aligning your reads to the transcriptome rather than the whole genome. Then align rest of the reads to the genome. TopHat has inbuilt capability for...
Forum: Bioinformatics 11-09-2012, 11:58 AM
Replies: 5
Views: 3,704
Posted By vinay052003
Also, just to bring it to the attention, each...

Also, just to bring it to the attention, each read group has to be unique for each library.
If you have same readgroup id (RGID) for two libraries, breakdancer will not be able to perform correctly.
Forum: Bioinformatics 10-11-2012, 10:49 AM
Replies: 8
Views: 2,324
Posted By vinay052003
If you are sure that all the bam files are from...

If you are sure that all the bam files are from the same library i.e. same insert size, then you can just merge and coordinate sort your bam files and run the BreakDancer.
Forum: Bioinformatics 09-28-2012, 12:16 PM
Replies: 0
Views: 1,228
Posted By vinay052003
Cuffdiff Sample v/s replicates FPKM

I ran cuffdiff on two multi-replicate samples. Cuffdiff reports FPKM for each sample as well as FPKM for each replicate.
I was wondering how does it calculate the sample FPKM from its replicate's ...
Forum: Bioinformatics 09-27-2012, 08:53 PM
Replies: 21
Views: 4,360
Posted By vinay052003
Hi guys, After reading through the discussion...

Hi guys,
After reading through the discussion above I am realizing that I should also try DESeq. I have two multi-replicate samples and ran cuffdiff on them. Cuffdiff produces a read count files in...
Forum: Bioinformatics 07-16-2012, 12:38 PM
Replies: 22
Views: 8,528
Posted By vinay052003
Hi catbus, Did you solve the "segmentation...

Hi catbus,
Did you solve the "segmentation fault" problem with tophat_report?
I tried running the updated version by compiling tophat 2.0.4 as well as using the pre-built binaries... but still...
Forum: Bioinformatics 07-16-2012, 09:43 AM
Replies: 22
Views: 13,679
Posted By vinay052003
Hi, When I want to run cutadapt or similar...

Hi,
When I want to run cutadapt or similar adapter trimming program, should I specify both of the Illumina PE adapters for each fastq file? How does program differentiate between the 5' and 3'...
Forum: Bioinformatics 07-11-2012, 11:10 AM
Replies: 11
Views: 3,778
Posted By vinay052003
I am sure you have run the tophat-fusion-post to...

I am sure you have run the tophat-fusion-post to remove the potential false positive. Beyond that, PCR experiments are the only way to validate the potential fusions.

"How do you go about to find...
Forum: Bioinformatics 06-27-2012, 12:20 PM
Replies: 0
Views: 685
Posted By vinay052003
bowtie2 genomic data

I was wondering if anyone has run the BowTie2 for genomic data.
My data is paired-end (100-100 bp) and comes from whole genome sequencing.

I am not sure at this stage if I should do end-to-end...
Forum: Bioinformatics 06-07-2012, 01:46 PM
Replies: 0
Views: 1,579
Posted By vinay052003
read trimming for tophat

Hi,
I am planning to run tophat on my paired-end RNA-Seq data library (75 bp length). Before running tophat, I checked the quality plots. The left end reads look fine but for the right end reads,...
Forum: De novo discovery 05-21-2012, 10:43 AM
Replies: 3
Views: 3,944
Posted By vinay052003
The difference between DNA and RNA-Seq assembly...

The difference between DNA and RNA-Seq assembly has been reviewed very well in http://www.ncbi.nlm.nih.gov/pubmed/21897427.

For DNA assembly you can use Velvet or ABySS. ABySS was actually...
Forum: Bioinformatics 05-16-2012, 11:55 AM
Replies: 34
Views: 12,939
Posted By vinay052003
Hi Richard, Please have a look at my previous...

Hi Richard,
Please have a look at my previous question. I was wondering what happens to those reads whose second is pair is unmapped and also missing from the bam file?
Thanks.
Forum: Bioinformatics 05-10-2012, 08:33 PM
Replies: 34
Views: 12,939
Posted By vinay052003
Hi Richard, Thanks a lot for the info. Works...

Hi Richard,
Thanks a lot for the info. Works perfectly.
Does this program make any assumptions about the input bam file (sorting on bam file). Does it also work if I have multiple alignments for...
Forum: Bioinformatics 05-10-2012, 01:22 PM
Replies: 34
Views: 12,939
Posted By vinay052003
Hi guys, I've run into a more complex problem...

Hi guys,
I've run into a more complex problem regarding bam to fastq conversion. Somehow my bam files have some unpaired reads mixed with the paired-end reads. I was running Picard but that seems to...
Forum: Bioinformatics 05-08-2012, 10:29 AM
Replies: 10
Views: 2,908
Posted By vinay052003
Thank GenoMax.. for some reason I can't find...

Thank GenoMax..
for some reason I can't find libboost_thread.so.1.48.0 on my system. My boost installation was successful though. I noticed that /my_boost_install_dir/lib is empty. Is this the...
Forum: Bioinformatics 05-07-2012, 01:47 PM
Replies: 10
Views: 2,908
Posted By vinay052003
Hi, I stills can not install Cufflinks. My make...

Hi,
I stills can not install Cufflinks. My make is successful but when I try to execute the cufflinks executable it gives me the following error:

error while loading shared libraries:...
Forum: Bioinformatics 05-07-2012, 12:23 PM
Replies: 10
Views: 2,908
Posted By vinay052003
Yes... I just noticed that... the source file has...

Yes... I just noticed that... the source file has been updated.
Forum: Bioinformatics 05-07-2012, 10:50 AM
Replies: 10
Views: 2,908
Posted By vinay052003
Hi segmagician, Thanks for the tip. If...

Hi segmagician,
Thanks for the tip. If possible, can you please provide the round.h? I am also having problem with that.
Thanks.
Forum: Bioinformatics 05-07-2012, 10:06 AM
Replies: 10
Views: 2,908
Posted By vinay052003
Hi Kopi-o, Did you figure out the installation...

Hi Kopi-o,
Did you figure out the installation problem yet? I am having another problem with the Eigen libray. I downloaded and copied the eigen-eigen-b23437e61a07/Eigen to a directory in my PATH...
Forum: RNA Sequencing 04-30-2012, 04:58 PM
Replies: 5
Views: 2,025
Posted By vinay052003
Yes.. Is there any good way?

Yes.. Is there any good way?
Forum: RNA Sequencing 04-30-2012, 04:17 PM
Replies: 5
Views: 2,025
Posted By vinay052003
That's a good idea. I thought of that as well....

That's a good idea. I thought of that as well. Actually in the end I also need the expression of each transcript. And after merging assemblies, in order to estimate the expression, I'll need to use...
Forum: RNA Sequencing 04-30-2012, 12:28 PM
Replies: 5
Views: 2,025
Posted By vinay052003
Merge from multiple libraries + tophat + cufflinks

Hi,
I have two paired-end sequencing RNA-Seq libraries. Both of them are from the same sample but prepared using different insert lengths. I've run tophat on both of them separately. Now I want to...
Forum: Bioinformatics 04-25-2012, 10:00 PM
Replies: 11
Views: 15,023
Posted By vinay052003
I'll give it a shot and let you know. Actually I...

I'll give it a shot and let you know. Actually I forgot to mention that I was using Mac Osx as well.

Thanks.
Forum: Bioinformatics 04-25-2012, 09:59 PM
Replies: 0
Views: 1,521
Posted By vinay052003
Picard SamToFastq is prior sort needed?

Hi,
I am trying to extract paired-end fastq files from a BAM file using Picard's SamToFastq. I was wondering if I need to sort my BAM file on query name before runnign SamtoFastq?

Thanks.
Forum: Bioinformatics 04-19-2012, 12:38 PM
Replies: 9
Views: 5,953
Posted By vinay052003
SVDetect v/s BreakDancer

Hi,
Has anyone had any experience with SVDetect and BreakDancer? I need some thoughts on their comparison in terms of performance and detection accuracy. I am mainly interested in detecting large...
Showing results 1 to 25 of 59

 


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