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Forum: RNA Sequencing 08-30-2017, 01:25 PM
Replies: 6
Views: 1,594
Posted By alec
I believe the low efficiency is due to a...

I believe the low efficiency is due to a combination of low of processivity of the reverse transcriptase and low efficiency of the template switching reaction, rather than initiation of RT. A...
Forum: Bioinformatics 06-07-2017, 10:01 AM
Replies: 6
Views: 1,827
Posted By alec
Removing...

Removing "/usr/lib/python3.4/:/usr/local/lib/python3.4/dist-packages" from the start of your PYTHONPATH should fix your immediate problem.

The problem is that bowtie2-build is using python 2.7...
Forum: Bioinformatics 06-07-2017, 08:22 AM
Replies: 6
Views: 1,827
Posted By alec
The line in question is: print("\nRemainder of...

The line in question is: print("\nRemainder of file ignored", file=sys.stderr)

This is valid syntax in python 3 but not 2. It looks like bowtie is using python 2.7 but it is trying to load...
Forum: Bioinformatics 09-07-2015, 08:50 AM
Replies: 2
Views: 1,143
Posted By alec
If you are looking to test whether mutations...

If you are looking to test whether mutations identified by WES are present in your single cells, you should be able to use standard SNP calling tools, although you might do better by doing a pileup...
Forum: Sample Prep / Library Generation 07-16-2015, 07:11 AM
Replies: 1
Views: 1,973
Posted By alec
Have a look at this paper: ...

Have a look at this paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128036
Forum: Bioinformatics 08-19-2013, 03:17 AM
Replies: 3
Views: 1,156
Posted By alec
You could compare their SNPs. The number of...

You could compare their SNPs. The number of differences due to somatic mutations should be relatively small, and you could filter out any that aren't in dbSNP. You'll also want to filter out cases...
Forum: RNA Sequencing 04-10-2013, 02:34 PM
Replies: 1
Views: 1,255
Posted By alec
To scale by total reads, go to View ->...

To scale by total reads, go to View -> Preferences -> Tracks and select Normalize Coverage Data. If you want some other normalization method (like upper-quartile), you would have to scale each track...
Forum: RNA Sequencing 12-28-2012, 06:18 AM
Replies: 14
Views: 4,659
Posted By alec
Yes, or set your environment some other way after...

Yes, or set your environment some other way after you rsh (like `source ~/.bash_profile` as GenoMax suggested)
Forum: RNA Sequencing 12-28-2012, 05:36 AM
Replies: 14
Views: 4,659
Posted By alec
Just a guess, but I think rsh loads your bashrc...

Just a guess, but I think rsh loads your bashrc file rather than bash_profile. If that doesn't work, try printing your environment with rsh and comparing to the local environment.
Forum: Bioinformatics 08-05-2012, 03:38 PM
Replies: 1
Views: 1,393
Posted By alec
It depends what you want to do. I've looked at...

It depends what you want to do. I've looked at HMMlib (http://www.cs.au.dk/~asand/?page_id=152) as well as GHMM but didn't seriously use either.

If all you need is something that will take a...
Forum: RNA Sequencing 07-20-2012, 03:23 PM
Replies: 17
Views: 8,423
Posted By alec
I think you need to do "export LD_LIBRARY_PATH"...

I think you need to do "export LD_LIBRARY_PATH" as well to make it visible to tophat
Forum: RNA Sequencing 07-20-2012, 10:50 AM
Replies: 17
Views: 8,423
Posted By alec
Either that file does not exist or it is not on...

Either that file does not exist or it is not on your library search path. Assuming it exists (it will normally be in boost/lib), the easiest way to change your library search path is:
...
Forum: Bioinformatics 07-20-2012, 06:53 AM
Replies: 11
Views: 3,715
Posted By alec
I'm thinking of being able to align sequences one...

I'm thinking of being able to align sequences one by one. For example, my reads often have custom barcodes at the beginning that need to be removed before alignment and written to a different file...
Forum: Bioinformatics 07-06-2012, 03:30 PM
Replies: 11
Views: 3,715
Posted By alec
If you go with the conversion tool, it would also...

If you go with the conversion tool, it would also be useful if it could convert from, say, hg18 to hg19 using a liftover file.

My vote would be for a Python wrapper to bowtie or bwa. For example,...
Forum: Bioinformatics 06-29-2012, 03:01 AM
Replies: 5
Views: 2,481
Posted By alec
You'll probably find it more convenient to use a...

You'll probably find it more convenient to use a single job array than submitting many jobs in a loop.
In your launch script do a single qsub:
qsub -t 0-$[${#result[@]}-1] test.sh
In test.sh the...
Forum: General 03-28-2012, 11:14 AM
Replies: 2
Views: 1,268
Posted By alec
http://genome.ucsc.edu/cgi-bin/hgPcr?command=start

http://genome.ucsc.edu/cgi-bin/hgPcr?command=start
Forum: General 02-08-2012, 12:40 PM
Replies: 3
Views: 2,204
Posted By alec
There has been some use of graph theory in...

There has been some use of graph theory in haplotyping. See:

http://dx.doi.org/10.1007/3-540-44676-1_15
http://bioinformatics.oxfordjournals.org/content/24/16/i153.abstract
Forum: Bioinformatics 02-01-2012, 06:17 AM
Replies: 5
Views: 2,137
Posted By alec
Visual Studio express edition is free. The...

Visual Studio express edition is free. The Windows SDK is also needed to compile 64 bit programs (see...
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