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Search: Posts Made By: Nowlan Freese
Forum: Bioinformatics 03-19-2015, 12:40 PM
Replies: 8
Views: 5,774
Posted By Nowlan Freese
We were able to get BWA to run correctly. ...

We were able to get BWA to run correctly.

The only thing we had to change was to use -a bwtsw when indexing the genome.

This was a little unexpected as we were using the tomato genome, which...
Forum: Events / Conferences 03-17-2015, 01:52 PM
Replies: 0
Views: 1,721
Posted By Nowlan Freese
Visualization of whole genome DNA methylation in IGB (March 25, 11:30am-12pm EST)

“Focus on a Feature: Visualization of whole genome DNA methylation data in IGB.”

This tutorial has ended. You can find the recording here (https://youtu.be/Hs-iNCGa1CA).

To follow along, you...
Forum: Bioinformatics 03-13-2015, 10:00 AM
Replies: 8
Views: 5,774
Posted By Nowlan Freese
The index and .sai files all have data, and we're...

The index and .sai files all have data, and we're using the most recent version of BWA (0.7.12).

We're going to try and rerun with -a bwtsw as an option while indexing, and we'll make sure all of...
Forum: Bioinformatics 03-13-2015, 09:17 AM
Replies: 8
Views: 5,774
Posted By Nowlan Freese
bwa index S_lycopersicum_chromosomes.fa ...

bwa index S_lycopersicum_chromosomes.fa

gunzip 141217HiSeq_Run_Sample_Sample_3_TTAGGC_L002_R1_001.fastq.gz
gunzip 141217HiSeq_Run_Sample_Sample_3_TTAGGC_L002_R2_001.fastq.gz

bwa aln...
Forum: Bioinformatics 03-13-2015, 09:00 AM
Replies: 8
Views: 5,774
Posted By Nowlan Freese
Alig, I'm getting the same error: ...

Alig,

I'm getting the same error:

[bwa_sai2sam_pe] fail to locate the index

What was the error that you encountered in your script, as I might be doing the same thing.

Thanks!
Forum: Events / Conferences 01-14-2015, 09:46 AM
Replies: 0
Views: 1,916
Posted By Nowlan Freese
ChIP-Seq Analysis and Visualization using Galaxy and IGB. (January 28, 11:30am-12pm E

“Focus on a Feature: ChIP-Seq Analysis and Visualization using Galaxy and IGB.”

This Focus on a Feature has finished. The recording can be found here (http://youtu.be/HqnQKgJd254).

The complete...
Forum: Events / Conferences 12-12-2014, 04:40 AM
Replies: 0
Views: 1,121
Posted By Nowlan Freese
Live on-line tutorial using Integrated Genome Browser (December 17, 2014 at 3:30pm)

“Focus on a Feature: Intro to All New Features in IGB 8.2.”

This Focus on a Feature has finished. The recording can be found here...
Forum: Events / Conferences 10-30-2014, 08:59 AM
Replies: 0
Views: 1,446
Posted By Nowlan Freese
Live on-line tutorial using Integrated Genome Browser (November 12, 2014 11:30am-12pm

“Focus on a Feature: RNA-Seq Alignment and Visualization using Galaxy and IGB.”

This Focus on a Feature has finished. The recording can be found here...
Forum: Events / Conferences 09-24-2014, 05:43 AM
Replies: 0
Views: 1,166
Posted By Nowlan Freese
Finished - On-line Tutorial "Alternative Splicing and Primer Design Using IGB"

Please join us for a live, on-line tutorial using the Integrated Genome Browser (IGB)

“Focus on a Feature: Alternative Splicing and Primer Design.”

This Focus on a Feature has finished. The...
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