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Search: Posts Made By: bioWizz
Forum: Bioinformatics 03-30-2016, 06:23 AM
Replies: 12
Views: 3,947
Posted By bioWizz
Hi Valeu, I have 10 sample 8 test and 2...

Hi Valeu,

I have 10 sample 8 test and 2 control for which I am trying to run oncocnv v6.4. I have configured ONCOCNV.sh file as per instructions given. It is throwing following error.



Any...
Forum: Bioinformatics 07-22-2015, 12:08 AM
Replies: 1
Views: 1,242
Posted By bioWizz
Bowtie large index error

Hello,
This is a duplicate from biostar. I have not found a solution to it. I build large index using bowtie "bowtie-build --large-index" for a multi fasta genome of approx 10 GB.
Index is...
Forum: Bioinformatics 09-08-2014, 04:17 AM
Replies: 0
Views: 557
Posted By bioWizz
Smile SHRiMP aligner options for unaligned (unmapped) reads

I am trying to align small RNA reads using SHRiMP using the command below

$ SHRiMP_2_2_3/bin/gmapper-ls -N 2 -o 1 -E input.fasta reference.fasta > output.sam

This gives me the .sam file output...
Forum: Ion Torrent 08-19-2014, 12:41 AM
Replies: 6
Views: 3,161
Posted By bioWizz
As you mentioned I had already tried running...

As you mentioned I had already tried running bowtie2 with local alignment mode, but it did not work.
Just looked into BWA-meth, it does say it supports single end reads. Looks like the tools I was...
Forum: Ion Torrent 08-18-2014, 10:00 AM
Replies: 6
Views: 3,161
Posted By bioWizz
Bismark for Ion Torrent

I am trying to use Bismark on targeted bisulphite sequencing done on PGM. Average read length is about ~102 maximum being ~190.
Bismark uses bowtie2 and running it with varying parameters gives me...
Forum: Introductions 07-03-2013, 11:17 PM
Replies: 0
Views: 444
Posted By bioWizz
Hello :)

Finally dived into analysis of NGS data. I am Sandeep from Manipal, India and will be working on the analysis of ION torrent PGM and proton data.
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