SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 20 of 20
Search took 0.00 seconds.
Search: Posts Made By: Brajbio
Forum: Metagenomics 07-05-2014, 03:36 AM
Replies: 8
Views: 15,361
Posted By Brajbio
Check out this tutorial for Pre-processing Paired...

Check out this tutorial for Pre-processing Paired end Illumina data for QIIME

https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/qiime-tutorial-3
Forum: Bioinformatics 02-05-2014, 07:10 AM
Replies: 18
Views: 5,395
Posted By Brajbio
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...
Forum: Bioinformatics 02-04-2014, 04:50 AM
Replies: 18
Views: 5,395
Posted By Brajbio
Hi Vishal, I tried to understand this issue...

Hi Vishal,

I tried to understand this issue what I understand is :

Since you have total 240 samples.

Now if you see the error which you get

.
.
Forum: Bioinformatics 02-04-2014, 03:20 AM
Replies: 18
Views: 5,395
Posted By Brajbio
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 :

.
.
.
[RUNNING:...
Forum: Bioinformatics 02-04-2014, 01:47 AM
Replies: 18
Views: 5,395
Posted By Brajbio
Hi Vishal, I am facing the similar problem. ...

Hi Vishal,

I am facing the similar problem.
Were you able to fix this issue?

Thanks, Braj
Forum: Bioinformatics 12-05-2013, 12:38 AM
Replies: 7
Views: 3,664
Posted By Brajbio
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...
Forum: Bioinformatics 12-04-2013, 11:43 PM
Replies: 7
Views: 3,664
Posted By Brajbio
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...
Forum: Bioinformatics 09-15-2011, 07:07 AM
Replies: 7
Views: 3,625
Posted By Brajbio
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...
Forum: Bioinformatics 09-15-2011, 06:52 AM
Replies: 6
Views: 3,884
Posted By Brajbio
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...
Forum: 454 Pyrosequencing 08-20-2011, 06:44 AM
Replies: 4
Views: 4,756
Posted By Brajbio
Could somebody explain in detail about...

Could somebody explain in detail about 'Singleton' reads and how they can be identified in the 'all reads' file. Also how useful it is to filter the singletons?
Forum: Bioinformatics 05-23-2011, 12:38 AM
Replies: 0
Views: 1,942
Posted By Brajbio
Quality Checks (QC) and filtering of NGS reads before further processing

Hi ,

I am working on the RNA-Seq workflow and i am using illumina reads.
I was wondering if i need to perform any kind of QC or read filtering before processing with Tophat tool in the pipeline....
Forum: Bioinformatics 05-10-2011, 10:35 PM
Replies: 30
Views: 12,255
Posted By Brajbio
can tophat be used for detection of gene fusion?

can tophat be used for detection of gene fusion?
Forum: Bioinformatics 05-10-2011, 10:25 PM
Replies: 30
Views: 12,255
Posted By Brajbio
Did some one has worked on FusionSeq or...

Did some one has worked on FusionSeq or FusionHunter. How are these tools comparatively with DeFuse in terms of performance and usability???
Forum: Bioinformatics 06-26-2010, 07:24 AM
Replies: 9
Views: 3,247
Posted By Brajbio
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,...
Forum: Bioinformatics 06-26-2010, 06:19 AM
Replies: 9
Views: 3,247
Posted By Brajbio
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...
Forum: General 06-19-2010, 05:25 AM
Replies: 2
Views: 9,007
Posted By Brajbio
Even i have a doubt regarding 'mate-pair inner...

Even i have a doubt regarding 'mate-pair inner distance' parameter option -r which is essential to give while running tophat with pair-ends.

Can someone help me how to determine the...
Forum: Bioinformatics 06-19-2010, 05:11 AM
Replies: 6
Views: 5,105
Posted By Brajbio
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...
Forum: Bioinformatics 06-02-2010, 05:00 AM
Replies: 6
Views: 5,105
Posted By Brajbio
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
Forum: Bioinformatics 06-02-2010, 01:40 AM
Replies: 6
Views: 5,105
Posted By Brajbio
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...
Forum: Bioinformatics 06-02-2010, 01:33 AM
Replies: 0
Views: 1,554
Posted By Brajbio
Tophat...Mapping reads against Reference with Bowtie [FAILED]

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...
Showing results 1 to 20 of 20

 


All times are GMT -8. The time now is 09:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO