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Forum: Illumina/Solexa 05-21-2013, 03:10 AM
Replies: 4
Views: 3,082
Posted By seqguy
I think you need to change the location of velvet...

I think you need to change the location of velvet and oases in "subprocess.Popen" section of the oases_pipeline.py script or put the excecutables in /usr/local/bin/ or /usr/bin/
Forum: RNA Sequencing 03-19-2011, 01:06 AM
Replies: 12
Views: 2,866
Posted By seqguy
could you please share the exact command you are...

could you please share the exact command you are using to run tophat?
Forum: RNA Sequencing 03-16-2011, 04:03 AM
Replies: 12
Views: 2,866
Posted By seqguy
1) Check if your GTF and reference genome files...

1) Check if your GTF and reference genome files are having same naming convention for chromosomes.
2) Reference genome index should be in colorspace.
3) Check if .csfasta and .qual files are having...
Forum: RNA Sequencing 03-14-2011, 05:29 AM
Replies: 12
Views: 2,866
Posted By seqguy
Have you created the bowtie index of your...

Have you created the bowtie index of your reference genome with -C option?
Forum: RNA Sequencing 03-14-2011, 04:40 AM
Replies: 12
Views: 2,866
Posted By seqguy
Could you please let me know the configuration of...

Could you please let me know the configuration of the system you are using to run this pipeline, the organism genome size and also if you are using root user or not.
Forum: RNA Sequencing 03-11-2011, 02:43 AM
Replies: 12
Views: 2,866
Posted By seqguy
Dear Lie You have to rearrange tophat...

Dear Lie

You have to rearrange tophat parameters to run it successfully. Tyr the below mentioned command:

./tophat -G <path to .gtf file> --color --quals <path to index folder/index prefix>...
Forum: Bioinformatics 12-14-2010, 10:49 AM
Replies: 9
Views: 7,369
Posted By seqguy
Dear Abhijit, why do u want to convert GFF...

Dear Abhijit,

why do u want to convert GFF to GTF, when you can easly download the GTF file itself from UCSC genome browser for drosophila
Forum: Bioinformatics 10-29-2010, 08:10 AM
Replies: 0
Views: 1,605
Posted By seqguy
problem in fragment library parallel assembly using ABySS

Hi Guys,

I have already installed ABySS on ROCKS 5.1 cluster and it is running perfectly fine on frontend/head node. I installed below mentioned softwares for ABySS:

mpfr-3.0.0.tar.gz...
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