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Forum: Bioinformatics 07-19-2010, 08:08 AM
Replies: 364
Views: 154,279
Posted By lparsons
Lightbulb Clearer icon

One suggestion would be to change the icon for tests that do not issue a warning or a fail to a blue "i" icon for info instead of the green check mark. That would make it obvious to people that...
Forum: Bioinformatics 06-29-2010, 09:43 AM
Replies: 15
Views: 4,016
Posted By lparsons
Excellent. Thanks for point that file out. I...

Excellent. Thanks for point that file out. I had installed it on OS X, thus it wasn't obvious those files were there. So far, it looking good.
Forum: Bioinformatics 06-28-2010, 12:26 PM
Replies: 15
Views: 4,016
Posted By lparsons
Question This looks like an excellent program and seems it...

This looks like an excellent program and seems it would be very useful for Chip-Seq data. However, I couldn't figure out how to add new genomes that aren't available on the server. Is there a way...
Forum: Bioinformatics 06-03-2010, 08:23 AM
Replies: 364
Views: 154,279
Posted By lparsons
Excellent utility Simon. Thank you. I'm...

Excellent utility Simon. Thank you.

I'm running into what looks like an old bug, however. I'm using FASTQC version 0.3.1 on a SunOS 5.10 server and I'm getting a HeadlessException. Any tips on...
Forum: Bioinformatics 03-22-2010, 07:18 AM
Replies: 35
Views: 25,682
Posted By lparsons
From the samtools directory, try: ./samtools...

From the samtools directory, try:

./samtools view my.bam
Forum: Illumina/Solexa 10-29-2009, 10:04 AM
Replies: 4
Views: 2,812
Posted By lparsons
Question When can I get away without a control lane?

Our users are interested in getting the highest throughput and lowest cost they reasonably can from the GA. As such, they would like to investigate eliminating the control lane from at least certain...
Forum: Bioinformatics 09-11-2009, 06:27 AM
Replies: 22
Views: 8,633
Posted By lparsons
What sort of error are you getting? You should...

What sort of error are you getting? You should be able to use:

fq_all2std.pl sol2std2 illumina_file.txt > standard_sanger_file.fastq
Forum: Bioinformatics 09-08-2009, 06:18 AM
Replies: 2
Views: 940
Posted By lparsons
I have the same problem. I'm not sure it is...

I have the same problem. I'm not sure it is going to be released, but there is a fixed version that was posted to these forums a while back:...
Forum: Bioinformatics 07-22-2009, 06:03 AM
Replies: 292
Views: 142,291
Posted By lparsons
I have noticed the same behavior with samtools...

I have noticed the same behavior with samtools tview. The biggest issue I have is with very deep alignments since I can find no way to scroll up or down in large chunks.

I also have a question...
Forum: Bioinformatics 05-19-2009, 07:40 AM
Replies: 22
Views: 8,633
Posted By lparsons
It sounds like you were able to get things...

It sounds like you were able to get things working. Let me know if you are still having trouble.

As for understanding the meaning of the symbols, do you mean you would like to get the...
Forum: Bioinformatics 05-05-2009, 08:56 AM
Replies: 99
Views: 34,866
Posted By lparsons
What would be useful would be a feature to export...

What would be useful would be a feature to export the coverage in a BED/WIGgle file that could be ready by GenomeBrowser or other similar tools. It would eliminate an extra step in my processing...
Forum: Illumina/Solexa 04-16-2009, 10:15 AM
Replies: 3
Views: 9,010
Posted By lparsons
Question Advice on analyzing barcoded samples with GERALD/ELAND

Does anyone have any advice on the bioinformatics side of dealing with barcoded data? Specifically, we are using the Illumina Pipeline 1.3.2.

I would like to be able to separate the reads based on...
Forum: Bioinformatics 04-01-2009, 02:05 PM
Replies: 99
Views: 34,866
Posted By lparsons
I ran the software on Windows, and was able to...

I ran the software on Windows, and was able to get it running. However, after converting a MAQ alignment to MVF, when I load the MVF file, I get an error:

Arithmetic operation resulted in an...
Forum: Bioinformatics 04-01-2009, 01:28 PM
Replies: 22
Views: 8,633
Posted By lparsons
It's a relatively simple change, since the format...

It's a relatively simple change, since the format is now (phred+64) and the standard is (phred+33).

So, I added a function to the fq_all2std.pl script in the MAQ scripts subdirectory:

sub...
Forum: Bioinformatics 04-01-2009, 09:09 AM
Replies: 99
Views: 34,866
Posted By lparsons
I tried to run MapView using Mono on a Mac OS X...

I tried to run MapView using Mono on a Mac OS X 10.5. It started, displayed the window briefly, the crashed with this error:

System.NotImplementedException: The requested feature is not...
Forum: Illumina/Solexa 03-30-2009, 07:26 AM
Replies: 24
Views: 25,439
Posted By lparsons
Does anyone have any advice on the bioinformatics...

Does anyone have any advice on the bioinformatics side of dealing with barcoded data? Specifically, we are using the Illumina Pipeline 1.3.2. The obvious simple solution is to separate the reads by...
Forum: Bioinformatics 03-30-2009, 06:37 AM
Replies: 50
Views: 15,746
Posted By lparsons
I was able to see line reads, though I'm a bit...

I was able to see line reads, though I'm a bit confused as to what the color scheme for the reference and reads means.

Also, I wasn't able to see depths view. Pressing F4 seems to have no effect.
Forum: Bioinformatics 03-27-2009, 07:42 AM
Replies: 50
Views: 15,746
Posted By lparsons
The 0.2.6 version fixed the "Bus error" on my...

The 0.2.6 version fixed the "Bus error" on my 64-bit Mac. Thank you for the fix and the excellent viewer. Let me know if I can help with testing, etc.
Forum: Bioinformatics 03-23-2009, 06:37 AM
Replies: 21
Views: 30,890
Posted By lparsons
You simply need to redirect the standard output...

You simply need to redirect the standard output (which is printing to your screen) to a file:

fq_all2std.pl fq2fa in.txt > out.fasta

See http://www.december.com/unix/tutor/redirect.html for...
Forum: Bioinformatics 03-11-2009, 03:19 PM
Replies: 292
Views: 142,291
Posted By lparsons
Thanks for the quick replies. I've tried with...

Thanks for the quick replies. I've tried with various values, etc. and the indexing step still seg faults. Any other ideas on debugging this? Perhaps using an older version? Thanks for any ideas.
Forum: Bioinformatics 03-10-2009, 02:25 PM
Replies: 292
Views: 142,291
Posted By lparsons
Yes, I sorted it just fine. In fact the indexing...

Yes, I sorted it just fine. In fact the indexing step will complain that the file isn't sorted.

One issue could be that I just realized that the ref_list file I gave during the import didn't...
Forum: Bioinformatics 03-10-2009, 02:12 PM
Replies: 292
Views: 142,291
Posted By lparsons
I imported an ELAND alignment and was able to...

I imported an ELAND alignment and was able to convert into SAM, then to BAM, then sort it. However, at the indexing step I too ran into a segmentation fault. I'm using the 0.1.2 version from the...
Forum: Bioinformatics 02-16-2009, 08:07 AM
Replies: 7
Views: 2,031
Posted By lparsons
I don't have a ton of experience with WIG files,...

I don't have a ton of experience with WIG files, but before FindPeaks I hadn't seen one that inserted new "start positions" within a chromosome track before. In other words, added lines like:
...
Forum: Bioinformatics 02-16-2009, 06:56 AM
Replies: 7
Views: 2,031
Posted By lparsons
I too ran into an issue with FindPeaks and IGB. ...

I too ran into an issue with FindPeaks and IGB. Basically, IGB complains that there is no track information for each fixedstep start location in the WIG file. From my review of the WIG file...
Forum: Bioinformatics 01-05-2009, 06:43 AM
Replies: 7
Views: 5,578
Posted By lparsons
You may be able to use the "Integrated Genome...

You may be able to use the "Integrated Genome Browser" IGB to view the WIG file. It is based on the opensource GenoViz SDK. You can find more information here: http://genoviz.sourceforge.net/
Showing results 1 to 25 of 28

 


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