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Search: Posts Made By: dnewkirk
Forum: Bioinformatics 08-05-2013, 05:41 PM
Replies: 3
Views: 1,183
Posted By dnewkirk
The FASTA files with the genomic sequence do not...

The FASTA files with the genomic sequence do not label what portions of the sequence are coding. There are other annotation files that have that information (such as the refFlat.txt or refGene.txt...
Forum: Bioinformatics 08-05-2013, 04:25 PM
Replies: 12
Views: 1,703
Posted By dnewkirk
The files are hard coded, ie, the script isn't...

The files are hard coded, ie, the script isn't using Getopt::Long to accept flags. So, you need to change the names in the script.
Forum: Bioinformatics 04-12-2013, 10:03 AM
Replies: 8
Views: 1,553
Posted By dnewkirk
You may be able to use Galaxy as well, which...

You may be able to use Galaxy as well, which would allow you to keep everything on Windows.

Link: https://main.g2.bx.psu.edu
Forum: Bioinformatics 02-19-2013, 09:02 PM
Replies: 11
Views: 9,095
Posted By dnewkirk
I had posted per the original question without...

I had posted per the original question without noticing the dates :). Either or works, but it may help someone who isn't as familiar with Perl on how to convert between file formats.
Forum: Bioinformatics 02-19-2013, 06:03 PM
Replies: 11
Views: 9,095
Posted By dnewkirk
#!/usr/bin/perl use strict; use warnings; ...

#!/usr/bin/perl

use strict;
use warnings;

# get file names from the command line
my ($input, $output) = @ARGV;

# exceptions and usage
if (!defined $input or !defined $output) {
Forum: Bioinformatics 06-28-2012, 01:02 PM
Replies: 11
Views: 5,352
Posted By dnewkirk
I think you will be far better off using a Linux...

I think you will be far better off using a Linux environment such as Ubuntu, which has a large, accessible community and level of documentation. They also have BWA, Bowtie, and many other tools...
Forum: RNA Sequencing 06-08-2009, 12:48 PM
Replies: 25
Views: 11,405
Posted By dnewkirk
Hello, If I can resurrect this thread...

Hello,
If I can resurrect this thread briefly, I've been having a little trouble with ERANGE 3.1. When I try to either annotate the genes or use the getfasta.py script to get the fasta sequence...
Forum: Epigenetics 04-23-2009, 02:18 PM
Replies: 20
Views: 63,510
Posted By dnewkirk
Bioconductor is in the process of developing an R...

Bioconductor is in the process of developing an R package (appropriately labeled chipseq currently) which should be released in the not too distant future. A working version can be had from the...
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