Forum: Metagenomics
07-05-2014, 03:36 AM
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Replies: 8
Views: 15,479
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Forum: Bioinformatics
02-05-2014, 07:10 AM
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Replies: 18
Views: 5,523
Hi Vishal,
Once you remove your target...
Hi Vishal,
Once you remove your target coordinates related to 'Y' chromosome from "probes.txt", then rerun the first step i.e RPKM calculation, and follow the next steps as instructed in the...
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Forum: Bioinformatics
02-04-2014, 04:50 AM
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Replies: 18
Views: 5,523
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Forum: Bioinformatics
02-04-2014, 03:20 AM
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Replies: 18
Views: 5,523
Hi Vishal,
Thanks for your reply.
I...
Hi Vishal,
Thanks for your reply.
I tried the way you suggested, but this time I am getting some new error at analysis step. The error which I am getting this time is :
.
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[RUNNING:...
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Forum: Bioinformatics
02-04-2014, 01:47 AM
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Replies: 18
Views: 5,523
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Forum: Bioinformatics
12-05-2013, 12:38 AM
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Replies: 7
Views: 3,745
Thanks sBeier, for the response.
No, I have...
Thanks sBeier, for the response.
No, I have not applied the options to accept concordant reads in bowtie1 run (is this option available in bowtie-0.12.3? Not sure if it is taken care by default on...
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Forum: Bioinformatics
12-04-2013, 11:43 PM
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Replies: 7
Views: 3,745
flagstat and rmdup issues
I too have observed the similar issue when I run 'flagstat' on the alignment files (.bam) resulted from the bowtie1 (with -I as 100 and -X as 300) and Tophat 2 (with -r as 200) respectively. My PE...
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Forum: Bioinformatics
09-15-2011, 07:07 AM
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Replies: 7
Views: 3,678
Hi I have bwa-0.5.9/solid2fastq.pl version. I...
Hi I have bwa-0.5.9/solid2fastq.pl version. I have two files SolF3.csfasta & SolF3_QV.qual which i want to convert in 'fastq'. After running the command as :
perl solid2fastq.pl Sol SolTest
I...
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Forum: Bioinformatics
09-15-2011, 06:52 AM
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Replies: 6
Views: 3,962
Hi I have bwa-0.5.9/solid2fastq.pl version. I...
Hi I have bwa-0.5.9/solid2fastq.pl version. I have two files SolF3.csfasta & SolF3_QV.qual which i want to convert in 'fastq'. After running the command as :
perl solid2fastq.pl Sol SolTest
I...
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Forum: 454 Pyrosequencing
08-20-2011, 06:44 AM
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Replies: 4
Views: 4,813
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Forum: Bioinformatics
05-23-2011, 12:38 AM
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Replies: 0
Views: 1,973
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Forum: Bioinformatics
05-10-2011, 10:35 PM
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Replies: 30
Views: 12,383
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Forum: Bioinformatics
05-10-2011, 10:25 PM
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Replies: 30
Views: 12,383
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Forum: Bioinformatics
06-26-2010, 07:24 AM
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Replies: 9
Views: 3,309
To my previous post i would like to add...
To my previous post i would like to add that......i had already successfully match this big size reads data once before with MAQ and even i have got the output as .map files, so i am pretty sure,...
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Forum: Bioinformatics
06-26-2010, 06:19 AM
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Replies: 9
Views: 3,309
I too got the similar error.
But...
I too got the similar error.
But surprisingly when i am feeding the single read input file (.bfq) of size 2.9 GB of each read 75 bp, its running sucessfully with MAQ but when i am giving the input...
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Forum: General
06-19-2010, 05:25 AM
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Replies: 2
Views: 9,138
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Forum: Bioinformatics
06-19-2010, 05:11 AM
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Replies: 6
Views: 5,282
I apologize for the delay
To John:
...
I apologize for the delay
To John:
Yeah when i type 'bowtie' on terminal, its displaying the help, so it is confirmed that bowtie is installed successfully.
To reaela :
Actually, it was...
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Forum: Bioinformatics
06-02-2010, 05:00 AM
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Replies: 6
Views: 5,282
To raela,
I had placed all the following...
To raela,
I had placed all the following requisite executables in root '/usr/bin'
1. bowtie
2. bowtie-inspect
3. bowtie-build
4. tophat
My input files : reads_1.fq, reads_2.fq
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Forum: Bioinformatics
06-02-2010, 01:40 AM
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Replies: 6
Views: 5,282
Bowtie...Error: could not execute Bowtie
Hi,
I am trying to run tophat with the sample data reads_1.fq and reads_2.fq.
I built the bowtie index successfully and moved the generated index files to the Bowtie indexes subdirectory. I run...
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Forum: Bioinformatics
06-02-2010, 01:33 AM
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Replies: 0
Views: 1,615
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