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Forum: Ion Torrent 01-28-2014, 10:52 PM
Replies: 122
Views: 110,816
Posted By ucpete
Boom! Thanks again! I'm guessing we'll have...

Boom! Thanks again! I'm guessing we'll have another update come AGBT next month (unfortunately I'm on the waiting list...).
Forum: Ion Torrent 01-28-2014, 10:21 PM
Replies: 122
Views: 110,816
Posted By ucpete
Thank you for your quick answer -- it's very much...

Thank you for your quick answer -- it's very much in line with my thinking. One of our primary concerns was about support and maintenance costs (rather than monetary costs). We do a fair amount of...
Forum: Ion Torrent 01-28-2014, 05:08 PM
Replies: 122
Views: 110,816
Posted By ucpete
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: 8,354
Posted By ucpete
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: 8,354
Posted By ucpete
I'm not sure what you're aiming for really -- I'm...

I'm not sure what you're aiming for really -- I'm not aware of BLAST having any special way of using paired-end information to make alignment more accurate, especially because your reads don't...
Forum: Bioinformatics 12-10-2012, 04:44 PM
Replies: 10
Views: 1,519
Posted By ucpete
Ah cool, good luck with the rest of your...

Ah cool, good luck with the rest of your analysis! I used emacs FWIW.
Forum: Bioinformatics 12-10-2012, 04:43 PM
Replies: 10
Views: 1,519
Posted By ucpete
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: 1,519
Posted By ucpete
I should also add that the above output skipped...

I should also add that the above output skipped the first line of your file, assuming it had a header line in it-- that's why 787 is missing.
Forum: Bioinformatics 12-10-2012, 04:31 PM
Replies: 10
Views: 1,519
Posted By ucpete
I just ran the same code on the same fragment of...

I just ran the same code on the same fragment of data and got the following output:

300, 1
429, 1
493, 1
513, 1
543, 1
544, 2
551, 1
563, 1
Forum: Bioinformatics 12-10-2012, 04:22 PM
Replies: 10
Views: 1,519
Posted By ucpete
It means that it can't find the third element in...

It means that it can't find the third element in the list after splitting the line on commas. Do all of your lines have 2 commas or does your data file look different?
Forum: Bioinformatics 12-10-2012, 01:37 PM
Replies: 10
Views: 1,519
Posted By ucpete
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: 1,011
Posted By ucpete
makeblastdb -in <genome.fasta> -dbtype nucl

makeblastdb -in <genome.fasta> -dbtype nucl
Forum: Bioinformatics 09-26-2012, 12:26 PM
Replies: 1
Views: 1,338
Posted By ucpete
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: 1,338
Posted By ucpete
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: 4,570
Posted By ucpete
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: 3,857
Posted By ucpete
In Python, and most programming languages, lists...

In Python, and most programming languages, lists are indexed starting at zero. So if you want the first, second, and seventh items, you want list[0], list[1], and list[6]. You're referencing objects...
Forum: Bioinformatics 06-13-2012, 05:33 PM
Replies: 24
Views: 3,857
Posted By ucpete
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: 3,857
Posted By ucpete
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: 3,857
Posted By ucpete
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: 5,272
Posted By ucpete
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: 3,857
Posted By ucpete
I'd just do it in Python. Let's say you have 10...

I'd just do it in Python. Let's say you have 10 fields on each line and you care about the 1st, 2nd, and 7th in terms of defining uniqueness.

inf = open("yourfile.txt")
outf =...
Forum: RNA Sequencing 06-07-2012, 05:20 PM
Replies: 6
Views: 4,570
Posted By ucpete
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: 4,570
Posted By ucpete
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: 4,570
Posted By ucpete
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: 3,521
Posted By ucpete
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...
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