Forum: Bioinformatics
01-08-2012, 11:53 AM
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Replies: 0
Views: 997
Counting of regions within a segment
Hello everyone. I have a scripting/coding question.
I'm trying to run an analysis to find the number of regions found within a particular segment length throughout a chromosome.
For instance:
...
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Forum: Bioinformatics
07-14-2011, 07:05 PM
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Replies: 4
Views: 1,662
Script Help
Hello everyone,
I've been racking my brain trying to create a script to make a certain file, but I have had no success in my attempts.
I have a file like this:
ACGCCGGCCA
GTGAATTGTA...
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Forum: Bioinformatics
01-29-2011, 02:03 PM
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Replies: 12
Views: 5,501
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Forum: Bioinformatics
01-24-2011, 03:00 PM
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Replies: 12
Views: 5,501
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Forum: Bioinformatics
01-24-2011, 07:29 AM
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Replies: 12
Views: 5,501
Simon,
Thank you for that rapid reply. After...
Simon,
Thank you for that rapid reply. After playing with it a little more I was able to generate the coverage plots based on the steps you laid out.
Can you please explain how you were able to...
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Forum: Bioinformatics
01-23-2011, 01:15 AM
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Replies: 12
Views: 5,501
How to generate coverage plots 101
Well I discovered how to generate these graphs. After learning their proper name "coverage plots" I was able to find a wealth of information. Yes, I'm pretty new to bioinformatics. haha
At any...
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Forum: Bioinformatics
01-12-2011, 02:09 PM
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Replies: 12
Views: 5,501
J,
Thanks for the recommendation of Mosaik...
J,
Thanks for the recommendation of Mosaik aligner. Looking at the documentation for it, it looks promising.
This will be a tomorrow project for me. I'll post up any results I'm able to come up...
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Forum: Bioinformatics
01-11-2011, 10:38 AM
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Replies: 12
Views: 5,501
Graphing Genome Distribution of Position Data
Hello everyone,
I would like to take my aligned small RNA data sets and create a graphical representation in order to see where the most and least expression takes place on a per chromosome or...
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Forum: Bioinformatics
09-01-2010, 01:18 PM
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Replies: 8
Views: 2,306
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Forum: Bioinformatics
09-01-2010, 12:06 PM
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Replies: 8
Views: 2,306
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Forum: Bioinformatics
08-30-2010, 09:54 AM
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Replies: 8
Views: 2,306
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Forum: Bioinformatics
08-26-2010, 09:32 AM
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Replies: 8
Views: 2,306
Grouping small RNAs for analysis
Hello everyone,
I'm trying to analyze small ncRNAs from Solexa sequencing data.
I've clipped, collapsed, and then aligned the sequences up to 15 times each to the genome.
The problem comes...
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Forum: Bioinformatics
08-15-2010, 11:53 PM
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Replies: 6
Views: 3,045
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Forum: Bioinformatics
08-15-2010, 07:26 PM
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Replies: 15
Views: 7,121
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Forum: Bioinformatics
08-12-2010, 01:50 AM
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Replies: 15
Views: 7,121
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Forum: Bioinformatics
08-08-2010, 11:13 PM
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Replies: 16
Views: 6,182
Martin,
Thanks for telling me how to fix the...
Martin,
Thanks for telling me how to fix the one failed problem. Actually I understand how to use Biopieces. For some reason when I type programs I've used before I could start the name of it in...
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Forum: Bioinformatics
08-08-2010, 02:58 AM
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Replies: 16
Views: 6,182
Well, honestly I'm not sure. I'm used to just...
Well, honestly I'm not sure. I'm used to just unzipping files and copying the binaries to the path so the way you install biopieces is a little new to me.
I think going through it this third time...
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Forum: Bioinformatics
08-07-2010, 06:04 PM
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Replies: 16
Views: 6,182
Martin,
I actually tried using biopieces...
Martin,
I actually tried using biopieces before. I've tried installing it on two separate occasions and have never been able to get it to work. I'd like to think I'm relatively decent with running...
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Forum: Bioinformatics
08-07-2010, 03:18 PM
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Replies: 4
Views: 2,202
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Forum: Bioinformatics
08-07-2010, 03:10 PM
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Replies: 4
Views: 2,202
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Forum: Bioinformatics
08-07-2010, 01:08 PM
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Replies: 4
Views: 2,202
Bowtie Strand Alignment
Nevermind. When I ran the alignments in Bowtie I forgot to remove the "-S" parameter.
*****************
I never really noticed this before, but Bowtie doesn't show - or + strand assignment....
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Forum: Bioinformatics
08-02-2010, 05:44 PM
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Replies: 15
Views: 7,121
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Forum: Bioinformatics
08-02-2010, 05:08 PM
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Replies: 15
Views: 7,121
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Forum: Bioinformatics
08-02-2010, 03:29 PM
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Replies: 15
Views: 7,121
Thank you both.
@adamdeluca:
join...
Thank you both.
@adamdeluca:
join 162Es/162Es.dsap.rfam.txt 721Es/721Es.dsap.rfam.txt -a1 -a2 -o 0 -o1.2 -o2.2 > 721Es.172Es.rfam
join: file 1 is not in sorted order
join: file 2 is not in...
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Forum: Bioinformatics
08-02-2010, 11:22 AM
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Replies: 15
Views: 7,121
Compare two files with Awk?
Hello everyone,
I have two files of ncRNAs from two different samples. I would like to compare them to each other by creating a single file that contains all the found ncRNAs in a file format such...
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