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Forum: Bioinformatics 02-21-2012, 07:18 AM
Replies: 17
Views: 6,730
Posted By bekkari
hi, can you please explain in detail, the...

hi,
can you please explain in detail, the option you provided here to convert bed to gtf?
especially what do you mean by "path_to_scripture", do we need to download any scripts?
Thanks in advance...
Forum: Bioinformatics 01-21-2010, 12:45 PM
Replies: 514
Views: 225,918
Posted By bekkari
Hi Ben, Can some one pleast let me know whether...

Hi Ben,
Can some one pleast let me know whether bowtie works with longer inserts (~20kb) between mate pairs?

Thanks
Forum: Bioinformatics 12-10-2009, 01:16 PM
Replies: 30
Views: 13,021
Posted By bekkari
"Seqmentation fault" error with cufflinks

Hi,
Did anyone figured out how to fix the error of segmentation fault that is arriving from running cufflinks. It occurs only when I use the annotation file in GTF format. The GTF file, I am...
Forum: Bioinformatics 11-13-2009, 10:29 AM
Replies: 292
Views: 161,824
Posted By bekkari
if you use BOWTIE as an alignment algorithm,...

if you use BOWTIE as an alignment algorithm, there is an option (--un) to dump all unmapped reads into a file.
Forum: Bioinformatics 11-10-2009, 10:58 AM
Replies: 292
Views: 161,824
Posted By bekkari
Does any one know about any tool/program to...

Does any one know about any tool/program to convert SAM output to BED format, if so please let me know
Forum: Bioinformatics 11-10-2009, 07:49 AM
Replies: 8
Views: 2,751
Posted By bekkari
Hi Ben, I was talking about clicking on any of...

Hi Ben,
I was talking about clicking on any of the link under "pre built indices" section of the page:
http://bowtie-bio.sourceforge.net/, will download the file but throws error while trying to...
Forum: Bioinformatics 11-10-2009, 05:57 AM
Replies: 8
Views: 2,751
Posted By bekkari
I had experienced same problem, so gave up and...

I had experienced same problem, so gave up and ended up building bowtie indexes on my own, but it took lot of time (more than 4 hrs)
Forum: Bioinformatics 11-06-2009, 11:09 AM
Replies: 292
Views: 161,824
Posted By bekkari
SAM format versions?

Can some one help me understand if there are any versions in SAM format. Cufflinks program works well with SAM format output by TOPHAT program but fails when the SAM output comes from Bowtie or bwa....
Forum: RNA Sequencing 11-06-2009, 10:13 AM
Replies: 2
Views: 3,111
Posted By bekkari
Yep, the same I heard from author

UCSC recognizes nothing but chr#, so have to you build your own indexes on chromosome sequences, which can downloaded from UCSC.
Forum: Introductions 11-05-2009, 04:35 AM
Replies: 1
Views: 1,351
Posted By bekkari
hello everybody

I am Kavitha working for Merck in Bioinformatics Division since 5 years. My current projects are about analyzing Sequencing data generated from Illumina/solexa platform, which obviously demands...
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