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Search: Posts Made By: koustavpal
Forum: Bioinformatics 08-18-2015, 11:56 PM
Replies: 4
Views: 1,971
Posted By koustavpal
Hi milo, I figured out the problem and got...

Hi milo,

I figured out the problem and got the entire pipeline working a long time ago, so it's a bit hard for me to remember how i did it. I'll try to help out as much as I can. So basically the...
Forum: Bioinformatics 07-23-2013, 10:21 PM
Replies: 4
Views: 1,971
Posted By koustavpal
bump

not to spam or anything but i really need help on this. so bump!
Forum: Bioinformatics 07-21-2013, 01:05 PM
Replies: 4
Views: 1,971
Posted By koustavpal
problem running multiz with MAF files

i downloaded some pairwise alignment files from UCSC in the axtnet format and converted these to the MAF format the general header looks like this

a score=21045.000000
s chr10 1454 357 + ...
Forum: Bioinformatics 06-11-2013, 10:19 PM
Replies: 4
Views: 1,843
Posted By koustavpal
Problem running TBA for MSA

Hi,

I have alignment data
hg19.panTro3.maf
hg19.gorGor3.maf
hg19.ponAbe2.maf
hg19.calJac3.maf
panTro3.gorGor3.maf
panTro3.ponAbe2.maf
panTro3.calJac3.maf
Forum: Bioinformatics 04-30-2013, 09:11 PM
Replies: 3
Views: 985
Posted By koustavpal
Usually most rna folding servers have a limit to...

Usually most rna folding servers have a limit to the length of sequence they will fold online, otherwise you can just download the vienna-rna package and just do it yourself, its a real cinch.

If...
Forum: Bioinformatics 04-30-2013, 08:48 PM
Replies: 0
Views: 1,703
Posted By koustavpal
Problem aligning Human Mitochondrial Transcriptome reads Cell 2011

Hi,

I am trying to align the human mitochondrial transcriptome reads using Bowtie and BWA, but after following the procedure in the article it fails to align accordingly to the hg18 genome (same...
Forum: Bioinformatics 02-19-2013, 07:46 PM
Replies: 0
Views: 1,216
Posted By koustavpal
BLAT gfServer Output format

It would be really helpful if someone can explain to me the output format of the BLAT gfServer, i searched a lot but i only came up with BLAT output formats but not the gfServer format, if anyone...
Forum: Bioinformatics 01-16-2013, 04:41 AM
Replies: 0
Views: 1,906
Posted By koustavpal
Exclamation TopHat coverage-search vs no-coverage-search option

So I am working on TopHat with RNA-Seq paired end illumina reads 100bp long, and the runtime is huge to say the least!!! the read files are 3.1gigs in size which means a total of 6gb worth of reads....
Forum: Bioinformatics 11-25-2012, 07:50 PM
Replies: 3
Views: 1,435
Posted By koustavpal
/* Copyright Vladimir Prus 2002. Distributed...

/* Copyright Vladimir Prus 2002. Distributed under the Boost */
/* Software License, Version 1.0. (See accompanying */
/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
...
Forum: Bioinformatics 11-25-2012, 07:48 PM
Replies: 3
Views: 1,435
Posted By koustavpal
char *getUser() /* Get user name */ { uid_t...

char *getUser()
/* Get user name */
{
uid_t uid = geteuid();
struct passwd *pw = getpwuid(uid);
if (pw == NULL)
errnoAbort("getUser: can't get user name for uid %d", (int)uid);
return...
Forum: Bioinformatics 11-25-2012, 07:16 PM
Replies: 3
Views: 1,435
Posted By koustavpal
Unhappy BLAT error

make[1]: Entering directory `/home/koustav/Desktop/blatSrc/lib'
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc...
Forum: Bioinformatics 11-02-2012, 09:00 PM
Replies: 1
Views: 1,320
Posted By koustavpal
Problem installing tophat

make all-recursive
make[1]: Entering directory `/home/tophat-2.0.5'
Making all in src
make[2]: Entering directory `/home/tophat-2.0.5/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall...
Forum: Bioinformatics 08-27-2012, 11:44 PM
Replies: 3
Views: 1,564
Posted By koustavpal
I have used bowtie2 to achieve the same, but our...

I have used bowtie2 to achieve the same, but our lab head is persistent on doing the same with maq. Therefore, i must use maq.
Forum: Bioinformatics 08-27-2012, 10:28 PM
Replies: 3
Views: 1,564
Posted By koustavpal
read length a problem when mapping with MAQ

Hi,

I have a file containing 36.8 million reads, as suggested in the MAQ manual I divided the file so that i had files containing 2 million reads. the minimum length of any read is 49bp, and the...
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