Forum: Ion Torrent
01-28-2014, 10:52 PM
|
|
Replies: 122
Views: 112,762
|
|
Forum: Ion Torrent
01-28-2014, 10:21 PM
|
|
Replies: 122
Views: 112,762
|
|
Forum: Ion Torrent
01-28-2014, 05:08 PM
|
|
Replies: 122
Views: 112,762
Can anyone update this question? We have a...
Can anyone update this question? We have a HiSeq2500 and a MiSeq here, and we have the opportunity to obtain an IonTorrent PGM essentially for free (we have to pay capital depreciation costs, but...
|
|
Forum: Bioinformatics
02-25-2013, 08:24 AM
|
|
Replies: 9
Views: 8,584
BLASTing each read file separately or BLASTing...
BLASTing each read file separately or BLASTing them in the same file will search the same amount of sequence. There will be no reduction in search space unless reads 1 and 2 are overlapping, and you...
|
|
Forum: Bioinformatics
02-22-2013, 04:33 PM
|
|
Replies: 9
Views: 8,584
|
|
Forum: Bioinformatics
12-10-2012, 04:44 PM
|
|
Replies: 10
Views: 1,553
|
|
Forum: Bioinformatics
12-10-2012, 04:43 PM
|
|
Replies: 10
Views: 1,553
Do you have any empty lines in the file?...
Do you have any empty lines in the file? Otherwise, I don't know what to tell you-- it totally worked as is for me. Assuming you don't have some underlying problem with your input file, this will...
|
|
Forum: Bioinformatics
12-10-2012, 04:33 PM
|
|
Replies: 10
Views: 1,553
|
|
Forum: Bioinformatics
12-10-2012, 04:31 PM
|
|
Replies: 10
Views: 1,553
|
|
Forum: Bioinformatics
12-10-2012, 04:22 PM
|
|
Replies: 10
Views: 1,553
|
|
Forum: Bioinformatics
12-10-2012, 01:37 PM
|
|
Replies: 10
Views: 1,553
Here's some Python code to do it for you,...
Here's some Python code to do it for you, assuming your file is called data.txt:
inputFile = open("data.txt")
inputFile.next() # skip that first header line
frequencyDict = {}
for line in...
|
|
Forum: Bioinformatics
12-10-2012, 01:25 PM
|
|
Replies: 2
Views: 1,045
|
|
Forum: Bioinformatics
09-26-2012, 12:26 PM
|
|
Replies: 1
Views: 1,392
I should add that one of the UTRs I'm...
I should add that one of the UTRs I'm particularly interested in has no detectable sequence homology to any other known UTR sequences, so the "fold by homologous inference" strategy is out the...
|
|
Forum: Bioinformatics
09-26-2012, 12:21 PM
|
|
Replies: 1
Views: 1,392
Looking for IRES in UTRs
I'm not sure if this is the right forum in which to be posting this question but I'm sure there are some RNA folding gurus out there. I've got some viral UTRs and I'm looking to see if there are any...
|
|
Forum: RNA Sequencing
06-26-2012, 05:22 PM
|
|
Replies: 6
Views: 4,635
On further review...
Upon further review, and after reading this (http://bridgecrest.blogspot.com/2011/08/use-of-log-log-plots-to-show-technical.html) post and its follow-up...
|
|
Forum: Bioinformatics
06-14-2012, 12:33 PM
|
|
Replies: 24
Views: 3,962
|
|
Forum: Bioinformatics
06-13-2012, 05:33 PM
|
|
Replies: 24
Views: 3,962
I'm guessing now that your file isn't...
I'm guessing now that your file isn't tab-delimited-- that it's space-delimited. Try changing to the split('\t') statement to just split(). I can't really help without much more information, sorry.
|
|
Forum: Bioinformatics
06-13-2012, 05:24 PM
|
|
Replies: 24
Views: 3,962
You'll be coding soon! It seems like your file...
You'll be coding soon! It seems like your file might have a header line. Try this instead:
inf = open("yourfile.txt")
outf = open("yourfile_unique.txt",'w')
uniqueValues = {}
for line in inf:
...
|
|
Forum: Bioinformatics
06-13-2012, 04:55 PM
|
|
Replies: 24
Views: 3,962
Type "python" from within the directory...
Type "python" from within the directory containing your file. Enter the above line-by-line, replacing "yourfile.txt" with whatever your file name is, and give it a descriptive output file name as...
|
|
Forum: General
06-13-2012, 04:37 PM
|
|
Replies: 11
Views: 5,392
I just keep a Word document open all day. Any...
I just keep a Word document open all day. Any code I write gets cat'ed and pasted into the notebook. Any commands I run, with output (provided it's not like 10 pages worth) get pasted into the...
|
|
Forum: Bioinformatics
06-13-2012, 04:28 PM
|
|
Replies: 24
Views: 3,962
|
|
Forum: RNA Sequencing
06-07-2012, 05:20 PM
|
|
Replies: 6
Views: 4,635
So actually in the original RPKM paper (I...
So actually in the original RPKM paper (I believe?) they take the log transform of the RPKM and calculate the Pearson correlations between two datasets that way. Seems reasonable, especially because...
|
|
Forum: RNA Sequencing
06-06-2012, 01:38 PM
|
|
Replies: 6
Views: 4,635
Hmmm. Thanks for that. I don't think Cohen's...
Hmmm. Thanks for that. I don't think Cohen's Kappa is applicable in my case because I'm not doing any qualitative categorization of the data. And my concern with Spearman is that my RPKM...
|
|
Forum: RNA Sequencing
06-05-2012, 04:28 PM
|
|
Replies: 6
Views: 4,635
Transcriptome similarity metric?
Can anyone think of a clever way to compare transcriptomes? Let's say for example I've got a transcriptome (in the form of RPKM values for a number of transcripts) that I consider to be a gold...
|
|
Forum: Sanger/Dye Terminator
06-01-2012, 11:27 AM
|
|
Replies: 4
Views: 3,592
That's really strange Sven, when I visit...
That's really strange Sven, when I visit http://lucy.sourceforge.net I get "The requested page is being migrated. This project/user is temporarily unavailable due to its data being migrated. Service...
|
