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Forum: Bioinformatics 03-02-2015, 10:35 AM
Replies: 7
Views: 1,817
Posted By jmw86069
fanli, many thanks! I would be interested in the...

fanli, many thanks! I would be interested in the modified htseq-count just for the sake of adding another tool to the bag of tricks.

I respect the intent of not counting those regions, and add...
Forum: Bioinformatics 03-02-2015, 06:51 AM
Replies: 7
Views: 1,817
Posted By jmw86069
It sounds like an HTSeqCount issue, my first...

It sounds like an HTSeqCount issue, my first guess would be that the GTF/gff file contains overlapping gene regions. Quick thing to check, view the gene models file directly or look at it in a genome...
Forum: Bioinformatics 10-15-2014, 09:12 AM
Replies: 3
Views: 1,647
Posted By jmw86069
With due respect, if your goal is to produce a...

With due respect, if your goal is to produce a plot which shows the overlaps/similarities of two transcriptomes, I'm not sure a Circos plot is the answer. If the transcriptomes are from different...
Forum: Bioinformatics 10-15-2014, 08:57 AM
Replies: 3
Views: 2,037
Posted By jmw86069
I'll give a quick shout out to Bpipe, I use it...

I'll give a quick shout out to Bpipe, I use it and recommend it. I have limited experience with make, but don't think I could lean on it as heavily as I do Bpipe to handle my workflows. If nothing...
Forum: Bioinformatics 09-10-2013, 04:13 AM
Replies: 3
Views: 5,331
Posted By jmw86069
Easiest fix is to call set.seed(123); before you...

Easiest fix is to call set.seed(123); before you run k-means, and/or before you run pheatmap. Depends upon which step(s) you want to be reproducible. If it is just the order on the heatmap itself,...
Forum: Bioinformatics 08-23-2013, 08:44 PM
Replies: 10
Views: 6,446
Posted By jmw86069
No bother at all, sorry I didn't get back to this...

No bother at all, sorry I didn't get back to this earlier in the day. The "lazy-load database 'P' is corrupt" sounds like a symptom of memory limits, or session corruption, or both. Occasionally...
Forum: Bioinformatics 08-23-2013, 05:07 AM
Replies: 10
Views: 6,446
Posted By jmw86069
Okay, a few things going on. First, do you want...

Okay, a few things going on. First, do you want the range from 0 to 0.4 to be solid white? Right now, your code will set white to ~0.2, since that is the midpoint between 0 and 0.4.

If you want...
Forum: Bioinformatics 08-23-2013, 04:26 AM
Replies: 10
Views: 6,446
Posted By jmw86069
Well the "breaks are not unique" part is...

Well the "breaks are not unique" part is straightforward, just try this:

bk <- unique(c(seq(-0.1,0, length=100), seq(0,0.4,length=100),seq(0.4,13,length=100)));

It is caused by concatenating...
Forum: Bioinformatics 08-23-2013, 03:20 AM
Replies: 10
Views: 6,446
Posted By jmw86069
Use the 'breaks' parameter of the heatmap.2()...

Use the 'breaks' parameter of the heatmap.2() function. Set it to a vector of values representing where the color breaks should be. I think you need n+1 breaks for colors, but in this rare case the...
Forum: Bioinformatics 08-01-2013, 06:20 AM
Replies: 8
Views: 10,992
Posted By jmw86069
A couple simple things to try that may help: 1....

A couple simple things to try that may help:
1. Creating a PDF instead of a JPEG will store a vector based image, which will not be blurry when you zoom in. You do have to adjust the font size...
Forum: Bioinformatics 05-15-2013, 08:35 PM
Replies: 15
Views: 4,591
Posted By jmw86069
The counts script that comes with DEXseq that Dr....

The counts script that comes with DEXseq that Dr. Anders referenced will produce counts per exon, which are then linked to annotated genes. No de novo detection is accomplished unless you provide a...
Forum: Bioinformatics 05-15-2013, 08:19 PM
Replies: 1
Views: 1,514
Posted By jmw86069
In future, it would be good to post a...

In future, it would be good to post a reproducible example, like including a small dummy data.frame for the "gene_lens" example you described. I made one up just to test, but I have no idea what your...
Forum: Bioinformatics 06-02-2012, 07:56 AM
Replies: 7
Views: 1,771
Posted By jmw86069
No second dariober's suggestion to use...

No second dariober's suggestion to use InParanoid. Its summary information and definitions of orthologs vs paralogs is quite useful. The key is that you must have annotated organisms to start with....
Forum: Bioinformatics 05-10-2012, 07:15 PM
Replies: 1
Views: 1,164
Posted By jmw86069
If you convert your table of repeats into BED...

If you convert your table of repeats into BED format, you can use BEDtools to count up the overlaps in bins across the genome. I created BED files tiled across the genome in whatever increments I...
Forum: Bioinformatics 05-10-2012, 07:01 PM
Replies: 1
Views: 3,334
Posted By jmw86069
There are other threads on Venn diagrams, but I...

There are other threads on Venn diagrams, but I think the short of it is that once you get beyond 4 sets (maybe even just 3), unless the visual message is blatantly obvious it's difficult to convey...
Forum: Bioinformatics 05-10-2012, 06:27 PM
Replies: 1
Views: 1,960
Posted By jmw86069
Try the 'limma' package methods like...

Try the 'limma' package methods like normalizeBetweenArrays(). If given a numeric matrix, it allows a few methods which aren't array-specific. The method 'scale' will scale to the median of each...
Forum: Bioinformatics 05-09-2012, 09:21 AM
Replies: 1
Views: 2,323
Posted By jmw86069
TargetScan v6.1 genome coordinates

I'm trying to find or create genome coordinates for TargetScan v6.1, released March 2012. UCSC provides a track from v5.1, but nothing newer. This thread (link UCSC mailing list...
Forum: Bioinformatics 07-03-2011, 08:36 PM
Replies: 6
Views: 2,244
Posted By jmw86069
Use NUCmer from the MUMmer package (available...

Use NUCmer from the MUMmer package (available from Sourceforge.) For large reference genomes, you have to split the reference into smaller pieces for it to fit in memory, then align everything to...
Forum: Bioinformatics 06-19-2011, 05:55 PM
Replies: 11
Views: 2,223
Posted By jmw86069
I agree with frozenlyse, and suggest running...

I agree with frozenlyse, and suggest running through some basic QC with something like the HOMER package. For example do you see clonal reads (symptom of PCR gone awry),GC bias (symptom of sequence...
Forum: General 03-19-2011, 06:48 AM
Replies: 1
Views: 1,582
Posted By jmw86069
Can you post an example URL (without the username...

Can you post an example URL (without the username and password)? My blind guess is to try surrounding the URL in double quotes:

wget "http://google.com"

The quotes protect you from the...
Forum: Bioinformatics 03-19-2011, 06:40 AM
Replies: 12
Views: 5,304
Posted By jmw86069
Great choice Ubuntu/BioLinux, though Fedora is...

Great choice Ubuntu/BioLinux, though Fedora is very solid also. For Linux you can find just about any answer on ubuntuforums.org, relevant to most distros. But keep a file in your home dir with the...
Forum: Bioinformatics 02-16-2011, 08:06 PM
Replies: 9
Views: 38,749
Posted By jmw86069
Always a fan of the linux one-liner, here is an...

Always a fan of the linux one-liner, here is an example for human ACTB gene using hg18:



UCSC's C.elegans tables don't include the knownGene and kg% tables, but some poking around ( using "show...
Forum: Bioinformatics 01-05-2011, 07:15 AM
Replies: 4
Views: 1,373
Posted By jmw86069
I agree with the OP that this issue is valuable...

I agree with the OP that this issue is valuable enough to capture the tricks of the trade somewhere. A few examples could be:
- compiling R optimized for the cpu and OS, whether on linux or OSX --...
Forum: Bioinformatics 12-14-2010, 07:00 PM
Replies: 4
Views: 2,372
Posted By jmw86069
I'm not sure what tools you're ideally wanting to...

I'm not sure what tools you're ideally wanting to use, but it seems that GTF may not be the most efficient format for the purpose you described as I understand it. (GTF would be way down my list of...
Forum: Bioinformatics 12-14-2010, 06:46 PM
Replies: 4
Views: 3,374
Posted By jmw86069
Enrico, thank you for posting the link to the...

Enrico, thank you for posting the link to the tool and reference, I'm interested in testing it out and providing feedback (if I have anything helpful to say!)

It looks to me that Argot2 is...
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