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Search: Posts Made By: Canadian_philosophy
Forum: Bioinformatics 06-06-2016, 06:23 AM
Replies: 244
Views: 103,621
Hi Brian, This command below worked for me. It...

Hi Brian,
This command below worked for me. It looks like if I name the output files, that doesn't work (e.g out1_hg19=,out2_hg19=,out1_mm10= etc)
.
If I use the basename command, the fastqs...
Forum: Bioinformatics 06-03-2016, 01:33 PM
Replies: 244
Views: 103,621
Hmmm.. so I pasted that from the stderr/out file...

Hmmm.. so I pasted that from the stderr/out file of the program, maybe that is how you formatted it there? This is how my command looks java...
Forum: Bioinformatics 06-03-2016, 01:20 PM
Replies: 244
Views: 103,621
Hi Brian, Thanks for responding. 1)...

Hi Brian,

Thanks for responding.

1) That is what I assumed, wanted to hear it from someone else here :)

2) These are things I am trying with bbsplit:

Trial 1 :
Forum: Bioinformatics 06-03-2016, 12:26 PM
Replies: 244
Views: 103,621
BBMap

1) I am interested in understanding how BBmap is simultaneously aligning reads to multiple genomes? Is this different from using bwa to align to multiple genomes sequencially?

2) I used Bbsplit to...
Forum: Bioinformatics 05-12-2011, 12:24 PM
Replies: 2
Views: 2,180
Thumbs down Hi there, Thanks for your reply. You are...

Hi there,

Thanks for your reply. You are right, I am trying to use STM for transcriptome assembly. I have assemblies from Velvet/oases and I am trying to use that to run the cd-hit-est and...
Forum: Bioinformatics 03-28-2011, 01:30 PM
Replies: 2
Views: 2,180
Question Scaffolding Translational mapping (STM) - velvet assembly summary?

Hello,

Has anyone used STM [http://genome.cshlp.org/content/early/2010/08/30/gr.103846.109.abstract[/URL] for velvet assembly summaries?

I am trying to use it and have issues (St9bad_alloc)...
Forum: Bioinformatics 07-29-2010, 09:40 AM
Replies: 10
Views: 32,232
Thanks Maubp, I just downloaded Emboss. I will...

Thanks Maubp, I just downloaded Emboss. I will get back if I bump into trouble.
Thanks very much.
Forum: Bioinformatics 07-29-2010, 07:36 AM
Replies: 0
Views: 2,511
Question Orthomcl Installation

Hello there,
I would like to know if anyone has installed Orthomcl Version 4 and used it? I have been trying to use it for a longtime - no luck:(

Thanks.
Forum: Bioinformatics 07-29-2010, 07:26 AM
Replies: 10
Views: 32,232
Exclamation BAM/SAM to Fasta

Hi there,

I have a couple of aligned sequences from BWA. I used samtools to get the BAM format. What I really need is the Fasta format of these aligned sequences. Is there a program that would...
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