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Forum: Bioinformatics 01-08-2012, 10:53 AM
Replies: 0
Views: 972
Posted By DrD2009
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:
...
Forum: Bioinformatics 07-14-2011, 06:05 PM
Replies: 4
Views: 1,628
Posted By DrD2009
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...
Forum: Bioinformatics 01-29-2011, 01:03 PM
Replies: 12
Views: 5,444
Posted By DrD2009
Is there a way for SeqMonk to recognize score...

Is there a way for SeqMonk to recognize score values such as those in BED or GFF formats?
Forum: Bioinformatics 01-24-2011, 02:00 PM
Replies: 12
Views: 5,444
Posted By DrD2009
It works perfectly and is much easier to perform...

It works perfectly and is much easier to perform in SeqMonk than having to convert files to another format.
http://i54.tinypic.com/27zhxyv.png

My lab members were wondering if there is a way to...
Forum: Bioinformatics 01-24-2011, 06:29 AM
Replies: 12
Views: 5,444
Posted By DrD2009
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...
Forum: Bioinformatics 01-23-2011, 12:15 AM
Replies: 12
Views: 5,444
Posted By DrD2009
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...
Forum: Bioinformatics 01-12-2011, 01:09 PM
Replies: 12
Views: 5,444
Posted By DrD2009
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...
Forum: Bioinformatics 01-11-2011, 09:38 AM
Replies: 12
Views: 5,444
Posted By DrD2009
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...
Forum: Bioinformatics 09-01-2010, 12:18 PM
Replies: 8
Views: 2,258
Posted By DrD2009
Martin, I think that may be exactly what...

Martin,

I think that may be exactly what I'm looking for. I'll go over it all and get back with you.


Thanks again,
Brandon
Forum: Bioinformatics 09-01-2010, 11:06 AM
Replies: 8
Views: 2,258
Posted By DrD2009
Thanks for that Martin. The samples I'm using are...

Thanks for that Martin. The samples I'm using are just small RNAs from an experiment and these are the results from Solexa sequencing. As far as comparison goes, I think what I want to try it pretty...
Forum: Bioinformatics 08-30-2010, 08:54 AM
Replies: 8
Views: 2,258
Posted By DrD2009
Martin, Would that allow me to go from this:...

Martin,

Would that allow me to go from this:
Chr2 4628 4644 TGAAAGACGAACAACT
Chr2 4628 4645 TGAAAGACGAACAACTG
Chr2 4628 4646 TGAAAGACGAACAACTGC
Chr2 4628 4647 TGAAAGACGAACAACTGCG...
Forum: Bioinformatics 08-26-2010, 08:32 AM
Replies: 8
Views: 2,258
Posted By DrD2009
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...
Forum: Bioinformatics 08-15-2010, 10:53 PM
Replies: 6
Views: 2,993
Posted By DrD2009
Did you remember to clip the adapters? From...

Did you remember to clip the adapters?

From experience I once aligned a Fastq file containing adapters and received a very similar low percentage alignment.

That's my guess.
Forum: Bioinformatics 08-15-2010, 06:26 PM
Replies: 15
Views: 6,998
Posted By DrD2009
Adam, Thanks for that solution.

Adam,

Thanks for that solution.
Forum: Bioinformatics 08-12-2010, 12:50 AM
Replies: 15
Views: 6,998
Posted By DrD2009
Adam, I was wondering if you could help me...

Adam,

I was wondering if you could help me out? I'm trying to do the exact same thing, but with larger files and by matching multiple columns.

File 1:...
Forum: Bioinformatics 08-08-2010, 10:13 PM
Replies: 16
Views: 6,095
Posted By DrD2009
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...
Forum: Bioinformatics 08-08-2010, 01:58 AM
Replies: 16
Views: 6,095
Posted By DrD2009
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...
Forum: Bioinformatics 08-07-2010, 05:04 PM
Replies: 16
Views: 6,095
Posted By DrD2009
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...
Forum: Bioinformatics 08-07-2010, 02:18 PM
Replies: 4
Views: 2,071
Posted By DrD2009
Not a problem.

Not a problem.
Forum: Bioinformatics 08-07-2010, 02:10 PM
Replies: 4
Views: 2,071
Posted By DrD2009
Ah. You can keep it up if you think it will be...

Ah. You can keep it up if you think it will be beneficial to others.
Forum: Bioinformatics 08-07-2010, 12:08 PM
Replies: 4
Views: 2,071
Posted By DrD2009
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....
Forum: Bioinformatics 08-02-2010, 04:44 PM
Replies: 15
Views: 6,998
Posted By DrD2009
:D That works. Thank you so much.

:D

That works. Thank you so much.
Forum: Bioinformatics 08-02-2010, 04:08 PM
Replies: 15
Views: 6,998
Posted By DrD2009
I guess I forgot to mention that not all ncRNAs...

I guess I forgot to mention that not all ncRNAs are found in both files. :(

Some ncRNAs are in one file and not the other. That is what caused the '-' in the combined file. Which was created...
Forum: Bioinformatics 08-02-2010, 02:29 PM
Replies: 15
Views: 6,998
Posted By DrD2009
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...
Forum: Bioinformatics 08-02-2010, 10:22 AM
Replies: 15
Views: 6,998
Posted By DrD2009
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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