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Search: Posts Made By: DineshCyanam
Forum: Bioinformatics 09-25-2012, 07:21 PM
Replies: 14
Views: 3,201
Posted By DineshCyanam
Yes, finding fusions in wild type is strange. Not...

Yes, finding fusions in wild type is strange. Not sure what is happening there. But I would look at the alignment that tophat-fusion-post generates (easier to look at the html output) showing the...
Forum: Bioinformatics 09-25-2012, 04:02 PM
Replies: 14
Views: 3,201
Posted By DineshCyanam
What flags did you use to run tophat-fusion-post?...

What flags did you use to run tophat-fusion-post? Did you use the --non-human flag?

-Dinesh
Forum: Bioinformatics 09-19-2012, 11:29 AM
Replies: 1
Views: 1,608
Posted By DineshCyanam
Yes, you are right. Tophat tries to align the...

Yes, you are right. Tophat tries to align the whole reads first and then the unmapped reads are split into small segments so in your case 9 (--segment-length 20) they would be split into 20bp...
Forum: Bioinformatics 09-13-2012, 05:17 AM
Replies: 56
Views: 12,564
Posted By DineshCyanam
Alright... So I ran the new PathSeq_BWA version...

Alright... So I ran the new PathSeq_BWA version and here are the results. I had ~65 million filtered reads and it took ~8 hours to finish and produced 177308 unmapped reads. This was run on 19 nodes...
Forum: Bioinformatics 09-12-2012, 11:52 AM
Replies: 56
Views: 12,564
Posted By DineshCyanam
Looks like there is a bug in...

Looks like there is a bug in Preprocessed_Reads.com file. Line 18 says exit and the script quits.
After commenting the line, the script runs fine.

@ n_para=$#

# Reading environmental...
Forum: Bioinformatics 09-12-2012, 06:31 AM
Replies: 56
Views: 12,564
Posted By DineshCyanam
Thanks for the update, Chandra. Will try it out...

Thanks for the update, Chandra. Will try it out and get back to you...

- Dinesh
Forum: Introductions 08-30-2012, 01:10 PM
Replies: 4
Views: 1,474
Posted By DineshCyanam
Hi and welcome to SEQanswers. Newbler is an...

Hi and welcome to SEQanswers.
Newbler is an commercial software and you would need a license to install it. Maybe you want to look at open source software for de novo assembly...
Here is a list:...
Forum: Bioinformatics 08-30-2012, 07:59 AM
Replies: 56
Views: 12,564
Posted By DineshCyanam
Hi Chandra, Any update on Pathseq_BWA? ...

Hi Chandra,
Any update on Pathseq_BWA?

-Dinesh
Forum: Bioinformatics 04-17-2012, 12:00 PM
Replies: 25
Views: 12,871
Posted By DineshCyanam
So I was able to reduce my runtime to ~4 hrs from...

So I was able to reduce my runtime to ~4 hrs from ~30 hrs by using the --no-coverage-search and --no-novel-indels flags.
Forum: Bioinformatics 04-16-2012, 06:37 AM
Replies: 1
Views: 4,341
Posted By DineshCyanam
Re-download the tophat-2.0.0 package as it was...

Re-download the tophat-2.0.0 package as it was updated and try again... (Same Version. Same file name)
Forum: Bioinformatics 04-16-2012, 06:28 AM
Replies: 25
Views: 12,871
Posted By DineshCyanam
Yes... Tophat 2 is taking extremely long (~ 30...

Yes... Tophat 2 is taking extremely long (~ 30 hrs)... particularly the Searching for junctions via segment mapping step as NicoBxl above observed. Here is my log.


Previous versions of Tophat...
Forum: Bioinformatics 03-01-2012, 08:26 AM
Replies: 10
Views: 5,876
Posted By DineshCyanam
Hi Cole, I see something similar with my data...

Hi Cole,
I see something similar with my data too. cuffdiff produces very few significant (Significant: Yes) genes although I have not compared with other methods. I am using cufflinks v1.3.0 but...
Forum: Bioinformatics 02-13-2012, 06:09 PM
Replies: 10
Views: 4,185
Posted By DineshCyanam
Hi Diya, Can you please post the command that...

Hi Diya,
Can you please post the command that you are using to run Tophat. Also, the Tophat version you are using is 1.2.0 which is more than an year old and there have been lots of changes since...
Forum: Bioinformatics 01-20-2012, 10:55 AM
Replies: 12
Views: 3,775
Posted By DineshCyanam
Exclamation That is wrong. cuffdiff can be used to compute...

That is wrong. cuffdiff can be used to compute the differential expression between two conditions. For two conditions, you need to give the sample names as comma separated values and differentiate...
Forum: Bioinformatics 12-28-2011, 12:23 PM
Replies: 6
Views: 11,901
Posted By DineshCyanam
For annotating the VCF file you can use the...

For annotating the VCF file you can use the Ensembl Variant Effect Predictor. It is very helpful and can also produce SIFT, PolyPhen and Condel consensus.
http://ensembl.org/tools.html

I would...
Forum: Site Feedback/Suggestions 12-02-2011, 10:10 AM
Replies: 7
Views: 16,353
Posted By DineshCyanam
Yes, the vBulletin apps are more work and a pain....

Yes, the vBulletin apps are more work and a pain. The mobile skin would work too but I believe apps likes Tapatalk have other features like keeping track of discussions, notifications and such. Also,...
Forum: Site Feedback/Suggestions 11-27-2011, 10:14 AM
Replies: 7
Views: 16,353
Posted By DineshCyanam
Question Support for Tapatalk?

Hi,
It would be great if SEQanswers has Tapatalk support. With many users now having smart phones and tablets, it would be easy to keep track of the threads and replies on the go using the Tapatalk...
Forum: Introductions 11-26-2011, 11:24 PM
Replies: 83
Views: 86,424
Posted By DineshCyanam
Thumbs up Thank You, Jon for fixing the bug and for the...

Thank You, Jon for fixing the bug and for the cufflinks_exclude files. :)

I was about to post about HiSeq data and Illumina's switch to Sanger quality scores (as I had to update your script to...
Forum: Introductions 11-26-2011, 08:28 PM
Replies: 83
Views: 86,424
Posted By DineshCyanam
I believe line #316 in the...

I believe line #316 in the RNAseq_MensFormal_Mac.sh should be as below. Or else no matter what user response you give (Yes/No), the tophat tag will always be set to TophatPE_GTF.

# TOPHAT_TAG...
Forum: Literature Watch 11-24-2011, 02:58 AM
Replies: 46
Views: 41,057
Posted By DineshCyanam
Well you still need to compare it with against a...

Well you still need to compare it with against a normal. See post #9 above.
40537

or

try CNVnator from Mark Gerstein's lab. You don't need to supply a ref file for CNVnator. More info and...
Forum: Literature Watch 11-24-2011, 02:38 AM
Replies: 46
Views: 41,057
Posted By DineshCyanam
Hi Parveen, The ref.hits would be from a...

Hi Parveen,
The ref.hits would be from a normal/control sample... or if you don't have one... You can get the normal bam file from the 1000 Genomes project.

-Dinesh
Forum: Introductions 11-20-2011, 04:33 PM
Replies: 83
Views: 86,424
Posted By DineshCyanam
Thanks a lot Jon for all the scripts... Really...

Thanks a lot Jon for all the scripts... Really appreciate your work... Makes my life super easy... I have lost count of how many times I have referred back to this thread...

- Dinesh
Forum: Bioinformatics 11-17-2011, 02:20 PM
Replies: 1
Views: 3,269
Posted By DineshCyanam
Yes, I am interested in knowing the same... Right...

Yes, I am interested in knowing the same... Right now I am using the commands given here: http://samtools.sourceforge.net/mpileup.shtml
Forum: Bioinformatics 08-02-2011, 12:38 PM
Replies: 6
Views: 5,367
Posted By DineshCyanam
Do the graphs make any sense? It would be great...

Do the graphs make any sense? It would be great if any of you can explain it to me.

I graphed the below region and here is what I get:
duplication...
Forum: Literature Watch 07-27-2011, 02:07 PM
Replies: 46
Views: 41,057
Posted By DineshCyanam
I have the same question too. It would be really...

I have the same question too. It would be really great if someone can shed some light on it.
Showing results 1 to 25 of 35

 


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