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Forum: Bioinformatics 04-04-2012, 06:27 AM
Replies: 0
Views: 1,219
Posted By jjw14
Question Problems importing GFFv3 Annotation into SeqMonk

I am using SeqMonk version 1.0 and trying to add annotation files in GFFv3 format available at ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/

Name Size Date Modified [parent directory]...
Forum: Bioinformatics 03-29-2012, 06:42 AM
Replies: 8
Views: 4,022
Posted By jjw14
Thanks, Simon. If I figure out how, I will post...

Thanks, Simon. If I figure out how, I will post the method I used here in case some other want to obtain similar data.

jjw
Forum: Bioinformatics 03-29-2012, 05:45 AM
Replies: 8
Views: 4,022
Posted By jjw14
Simon, Thank you for the information. Sorry...

Simon,

Thank you for the information. Sorry for the delay in my response.

I agree with you that the UCSC Table Browser is a great resource, and I have used it before for exporting specific...
Forum: Bioinformatics 03-27-2012, 09:32 AM
Replies: 8
Views: 4,022
Posted By jjw14
Question SeqMonk: Export features (e.g. CpG Islands) from Ensembl for import into SeqMonk?

Hello,

I am using SeqMonk to view reads mapped to a genome. I would like to import an extra annotation set (CpG Islands) to use in my analysis as is described in the SeqMonk help file under the...
Forum: Bioinformatics 03-22-2012, 10:51 AM
Replies: 9
Views: 23,784
Posted By jjw14
Thumbs up Thanks Peter, I'll take a look. jjw14

Thanks Peter,

I'll take a look.

jjw14
Forum: Bioinformatics 02-16-2012, 07:06 AM
Replies: 9
Views: 23,784
Posted By jjw14
Thumbs up Thanks for the quick reply, John. No doubt,...

Thanks for the quick reply, John.

No doubt, you've saved me a lot of frustration. I appreciate it.

jjw
Forum: Bioinformatics 02-16-2012, 06:44 AM
Replies: 9
Views: 23,784
Posted By jjw14
Question John, I'm running into the same problem that...

John,

I'm running into the same problem that you had. The NCBI Sus scrofa genome FTP site provides .asn, .fa, .gbk, .gbs, and .mfa files for each chromosome (last updated 10-12-2011).

Were...
Forum: General 02-03-2012, 10:38 AM
Replies: 10
Views: 2,814
Posted By jjw14
Thumbs up Looks like the DNS issue has been resolved. Ten...

Looks like the DNS issue has been resolved. Ten minutes ago I couldn't access the domain www.bioinformatics.bbsrc.ac.uk, but just now I was able to download the latest copy of SeqMonk.

Thanks!...
Forum: Bioinformatics 04-19-2011, 12:58 PM
Replies: 0
Views: 8,587
Posted By jjw14
Question RNA-seq Galaxy workflow for PE barcoded samples?

Hello,

I am working with RNA-seq Illumina data files in Galaxy (http://main.g2.bx.psu.edu/). The files are 100bp paired-end reads, multiplexed with barcoding to distinguish samples. There are...
Forum: Bioinformatics 11-16-2010, 02:48 PM
Replies: 10
Views: 8,660
Posted By jjw14
Very much appreciated! JJW

Very much appreciated!
JJW
Forum: Bioinformatics 10-07-2010, 01:19 PM
Replies: 1
Views: 2,685
Posted By jjw14
Bowtie to align reads to single chromosome or region?

Question for the Bowtie experts out there:

If I was to generate a bowtie index from a single chromosome, rather than the full genome, and align my reads to this "chromosome-index", would you...
Forum: Bioinformatics 10-05-2010, 01:43 PM
Replies: 10
Views: 8,660
Posted By jjw14
Hi Jonathan, I hope the option of serving...

Hi Jonathan,

I hope the option of serving the files from your desktop works. My desktop computer is a Mac, so I was using the Apache web server in OS X. The slow transfer wasn't a software...
Forum: Bioinformatics 10-05-2010, 10:20 AM
Replies: 10
Views: 8,660
Posted By jjw14
Jonathan, Yes and no. I found a solution,...

Jonathan,

Yes and no. I found a solution, but it's not free. I purchased an account from a web hosting service that allows SFTP transfers for $10 a month. Peanuts to some, I know. In the end,...
Forum: Bioinformatics 09-29-2010, 11:46 AM
Replies: 4
Views: 1,386
Posted By jjw14
I second the recommendation for SeqMonk. Very...

I second the recommendation for SeqMonk. Very flexible options to analyze peak data. The author of the program posts regularly in the SeqAnswers forums and is really helpful.
Forum: Bioinformatics 08-24-2010, 07:35 AM
Replies: 8
Views: 6,380
Posted By jjw14
Great information. I had actually downloaded the...

Great information. I had actually downloaded the SeqMonk dmg to my Mac about two weeks ago, but wasn't sure if I had enough RAM (4 GB) to run it, so I defaulted to using the available tools on our...
Forum: Bioinformatics 08-24-2010, 06:56 AM
Replies: 8
Views: 6,380
Posted By jjw14
Thanks for the response. I appreciate it. jjw

Thanks for the response. I appreciate it.
jjw
Forum: Bioinformatics 08-24-2010, 06:55 AM
Replies: 8
Views: 6,380
Posted By jjw14
Thumbs up Thanks very much. Your description of the...

Thanks very much. Your description of the "independent peaks" or peak "frequency" for MeDIP versus ChIP is exactly the type information I was interested in.

I'm using MACS for peak detection. ...
Forum: Bioinformatics 08-20-2010, 11:51 AM
Replies: 8
Views: 6,380
Posted By jjw14
Bumping shorter version of original post....

Bumping shorter version of original post. Apologies if this is bad form. Just looking for a bit of advice. Much appreciated.
jjw
Forum: Bioinformatics 08-18-2010, 07:50 AM
Replies: 8
Views: 6,380
Posted By jjw14
MeDIP-seq versus ChIP-seq analyses?

I've shortened my previous post in hopes of getting a response:

- I am mapping MeDIP sequence reads (Illumina GAII) with Bowtie and using MACS for peak finding.
- Question 1: Should only...
Forum: Bioinformatics 07-29-2010, 06:17 AM
Replies: 0
Views: 2,432
Posted By jjw14
Peak finding with MACS: Questions on # of reads and "strand bias"

Hi,

I have ChIP-seq data generated using a methylcytosine antibody and the Illumina GAII. For each sample, I have an input control (IC) and an immunoprecipitated (IP) sample. Bowtie was used...
Forum: Bioinformatics 07-16-2010, 05:54 AM
Replies: 5
Views: 3,539
Posted By jjw14
Yes, UCSC's Table Browser does have BED format as...

Yes, UCSC's Table Browser does have BED format as a file output option. I've been reading the excellent BEDTools documentation by the developer, Aaron Quinlan, that you mentioned. I have to agree...
Forum: Bioinformatics 07-15-2010, 10:45 AM
Replies: 5
Views: 3,539
Posted By jjw14
That does sound more direct than the Rube...

That does sound more direct than the Rube Goldberg method I was attempting.

Just so I am clear, would something like this be correct:

$ intersectBed -a MyReads.bed -b CpGIslands.bed

where...
Forum: Bioinformatics 07-15-2010, 09:32 AM
Replies: 5
Views: 3,539
Posted By jjw14
UCSC Table Browser: Please tell me there is an easier way...

With the advice of several members of the SEQanswers forum and a lot of reading, I was able to go from Illumina ChIP-seq reads to viewing alignments in the UCSC Genome Browser - Thanks! Also, a huge...
Forum: Bioinformatics 07-09-2010, 11:46 AM
Replies: 4
Views: 5,009
Posted By jjw14
Thanks for the feedback. You are correct. If I...

Thanks for the feedback. You are correct. If I look up the http address of the file I am serving from a computer on campus, I can see and download the file fine. However, when I tried to access...
Forum: Bioinformatics 07-08-2010, 12:35 PM
Replies: 4
Views: 5,009
Posted By jjw14
Uploading BAM Track to UCSC Genome Browser

I have built a bowtie index from the Nov. 2009 Sus scrofa draft assembly (SGSC Sscrofa9.2) that I downloaded from the UCSC website. I aligned my Illumina sequence reads to this index and output the...
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