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Forum: Bioinformatics 08-16-2012, 01:38 PM
Replies: 0
Views: 10,198
Posted By apratap
Smile Question: Metatranscriptome assemblers

Hi Everyone

Just wanted to know what assemblers/pipelines people are using for assembling metatranscriptomes. We have data sets from 200 million to few billion reads and are interested to know the...
Forum: Bioinformatics 08-09-2012, 09:32 AM
Replies: 1
Views: 4,106
Posted By apratap
Smile cuffdiff : time series and cummeRbund analysis

Hi Guys

I would like to know what the --time-series option in cuffidff does and how it is different from standard differential analysis cufflinks does. I have a time series RNA-Seq experiment...
Forum: Bioinformatics 06-02-2012, 11:37 AM
Replies: 4
Views: 1,235
Posted By apratap
slink Can you post the full command as well...

slink

Can you post the full command as well as the bowtie version ?

-A
Forum: Bioinformatics 05-18-2012, 11:06 PM
Replies: 10
Views: 3,388
Posted By apratap
The current version if SNAP as I understand is...

The current version if SNAP as I understand is mainly supported for human genome...I had a list of trouble getting it to run on other genomes and finally gave it..may need some more time to turn into...
Forum: Bioinformatics 05-15-2012, 12:09 PM
Replies: 2
Views: 2,678
Posted By apratap
Smile Metatranscriptomes assemblers

Hi Everyone

Just wanted to know what assemblers/pipelines people are using for assembling metatranscriptomes. We have data sets from 200 million to few billion reads and are interested to know the...
Forum: Bioinformatics 05-15-2012, 10:03 AM
Replies: 1
Views: 1,653
Posted By apratap
Smile Question: Advice : building transcript models using cufflinks

Hi Guys

Keeping it short I want to know which is a better approach for building transcripts models using cufflinks.

If I have an older set of gene models (as a .gtf file) for a species and some...
Forum: RNA Sequencing 04-30-2012, 03:13 PM
Replies: 4
Views: 4,999
Posted By apratap
Strangely enough I have got this error for the...

Strangely enough I have got this error for the first time ..

[2012-04-30 16:01:30] Preparing reads
[FAILED]
Error running 'prep_reads'
terminate called after throwing an instance of 'int'

...
Forum: Bioinformatics 02-09-2012, 12:39 PM
Replies: 5
Views: 4,440
Posted By apratap
Hi maubp hers the URL for biostar corss...

Hi maubp

hers the URL for biostar corss posting.

http://biostar.stackexchange.com/questions/17232/application-of-pacbio-based-cdna-data-in-rna-seq-analysis

-Abhi
Forum: Bioinformatics 02-08-2012, 03:33 PM
Replies: 5
Views: 4,440
Posted By apratap
Smile Application of PacBio based cDNA data in RNA-Seq analysis

Hi Everyone

Just wanted to know how people are using cDNA sequence data obtained from PacBio. Just curious to see and understand downstream applications in conjunction to Illumina cDNA data. Any...
Forum: Bioinformatics 01-31-2012, 08:27 AM
Replies: 5
Views: 4,117
Posted By apratap
One way to do it is two extract RNA in two steps....

One way to do it is two extract RNA in two steps. 1.) Capture Poly-A tail 2.) Perform ribosomal depletion on the leftover sample and the leftover should contain Poly A-.

When we do this we still...
Forum: Bioinformatics 11-03-2011, 07:21 PM
Replies: 2
Views: 2,427
Posted By apratap
@Wallysb01 : Thanks for your reply. I am...

@Wallysb01 : Thanks for your reply.

I am not sure how -j could help as the number of reads that seem to mapping to intronic regions for this particular gene is very less compared to spliced...
Forum: Bioinformatics 11-03-2011, 01:02 PM
Replies: 2
Views: 2,427
Posted By apratap
Smile cufflinks not able to assemble transcripts in high read coverage area

Hey Guys

I am using cufflinks for building transcriptome. I am seeing some regions where in-silico model predictions is re-affirmed by RNA-Seq data but however cufflinks or scripture is not able...
Forum: Bioinformatics 06-29-2011, 09:47 AM
Replies: 27
Views: 10,400
Posted By apratap
Ok good to know. I will start a new thread for...

Ok good to know. I will start a new thread for my question then.

Best,
-Abhi
Forum: Bioinformatics 06-29-2011, 09:46 AM
Replies: 0
Views: 1,779
Posted By apratap
Smile Rescuing Orphaned reads with local alignment within a radius of mapped mate

So we have a dataset of variable insert library as we are sequencing the 5' and 3' end of transcripts. As a result the distance between the mates( <--- --->) is dependent on the length of transcript....
Forum: Bioinformatics 06-28-2011, 09:44 AM
Replies: 27
Views: 10,400
Posted By apratap
Hi Nils Just wondering can SRMA be used for...

Hi Nils

Just wondering can SRMA be used for rescuing orphaned reads. So we have a dataset of variable insert library as we are sequencing the 5' and 3' end of transcripts. As a result the distance...
Forum: Bioinformatics 06-23-2011, 01:51 PM
Replies: 5
Views: 4,853
Posted By apratap
Any idea why BWA needs reads to be inner...

Any idea why BWA needs reads to be inner directional (---> <---) for it to map them.

I guess Tophat will not work as the read lengths are variable and as per my understanding of the version I used...
Forum: Bioinformatics 06-23-2011, 01:37 PM
Replies: 5
Views: 4,853
Posted By apratap
Hi Jon Thanks for your reply. The protocol...

Hi Jon

Thanks for your reply. The protocol is not standard we are trying to sequence the ends of transcripts using Mate Pair technique.

I data that I get after linker removal is of variable...
Forum: Bioinformatics 06-23-2011, 09:42 AM
Replies: 5
Views: 4,853
Posted By apratap
Smile BWA behaviour with Mate Pair data + Multi read mapping

Hi All

PS: This message was also posted on BWA mailing list but I did not get any response.


I am not able to logically understand why BWA is/not able to work natively
with mate pair data. ...
Forum: Bioinformatics 04-07-2011, 02:35 PM
Replies: 0
Views: 1,771
Posted By apratap
Smile Normalizing Single Cell libraries

Hi Guys

Just wondering if you have some experience with normalizing single cell libraries correcting for the MDA (Multiple Displace Amplification) bias.

I would love to hear about the...
Forum: General 03-16-2011, 12:27 PM
Replies: 0
Views: 1,257
Posted By apratap
Smile How to check for Library swap between similar species

We have some libraries which we multiplexed for plant and on a
separate experiment for soil metagenome. We have a doubt that during
library preparation one or more of the libraries were swapped or...
Forum: Bioinformatics 03-03-2011, 02:52 PM
Replies: 2
Views: 2,563
Posted By apratap
Hi Smith Thanks for correcting me. I indeed...

Hi Smith

Thanks for correcting me. I indeed meant cluster of clusters i.e a region on the flowcell. What I am not sure what size regions should I limit myself to.

I think what you suggest...
Forum: Bioinformatics 03-03-2011, 01:31 PM
Replies: 2
Views: 2,563
Posted By apratap
Smile binning Illumina reads by clusters on flowcell

Just wondering is it possible to group the reads by the cluster they
came from on the flowcell. We want to do so to get an idea of regions(clusters)
contributing to low/high quality reads and...
Forum: Bioinformatics 03-03-2011, 01:28 PM
Replies: 31
Views: 18,551
Posted By apratap
You could also try : ...

You could also try :

http://genome.sph.umich.edu/wiki/VcfCodingSnps

The requirement is that the input snps be in VCF format.

-Abhi
Forum: Bioinformatics 01-27-2011, 09:55 AM
Replies: 3
Views: 13,013
Posted By apratap
Hi rdu I see these messy N's always in the...

Hi rdu

I see these messy N's always in the Illumina data. I think it could mean variety of different things but this is just my interpretation. Mianly I think when the base caller is not able to...
Forum: Illumina/Solexa 09-24-2010, 09:55 AM
Replies: 17
Views: 6,912
Posted By apratap
Hi mgogol As far as the propriety pipeline...

Hi mgogol

As far as the propriety pipeline of Illumina are concerned they remain to be same but in our experience,we have seen significant increase in the processing times as the raw data goes up...
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