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Overlapping and non-Overlapping pair-end reads with Tophat senpeng Illumina/Solexa 4 10-16-2011 07:43 PM
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Old 02-22-2011, 09:43 AM   #21
ACTGangster
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Running 2.7 and this doesn't happen. Do you have setuptools installed?

Try typing import setuptools in the python console.

If not, download setup_tools and install it using python2.7
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Old 02-22-2011, 10:14 AM   #22
gpcr
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Thanks a tonn.
It worked after importing setuptools.
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Old 02-22-2011, 10:22 AM   #23
ACTGangster
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no problem. email me if you need anything else: adavisr at ufl dot edu.

Also, please cite the website if it works. https://github.com/audy/stitch
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Old 03-12-2011, 10:37 PM   #24
jstjohn
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I have a working draft C program to do adapter stripping/ paired-end merging similar to stitch and SHERA for large gzipped datasets. It looks like it processes somewhere around 20M 100x2 pairs per hour. Its available here if anyone is interested:

https://github.com/jstjohn/SeqPrep

I don't have correctness statistics available, but the program can copy a subset of the merged reads into a human-readable aligned format so you can sanity check the settings.
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Old 03-30-2011, 08:04 PM   #25
christophe
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Question Overlapping and non-Overlapping pair-end reads with Tophat

Quote:
Originally Posted by Cole Trapnell View Post
As of TopHat 1.0.13, you should be able to specify a negative inner distance of -30. TopHat does map the reads independently, and has a different algorithm from Bowtie for handling the ends. The coverage.wig file display depth of read coverage, not depth of physical coverage, so those bases will be double counted, as you suggest. However, Cufflinks operates at the fragment level, not the read level, and so should do the right thing here.
Hi Cole,
First, According to the quote above, we may use negative inner distance. If I set it up at -30 and the stddev at 10, this mean tophat will look for overlapping of size 20 to 40.
Am I correct?


Second
if I have a mix of pair-ended reads such as some read pairs are overlapping some are not;
---> May I set up the inner distance to 10 and then the std deviation for the inner distance at 50 for example?
---> In that case, will Tophat look for inner distance from -40 to +60? (-40 meaning an overlap of 40)

Thanks a lot in advance for your help.
Chris***

Last edited by christophe; 03-30-2011 at 08:06 PM. Reason: title modification
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Old 04-29-2011, 11:51 AM   #26
luc
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Default Thanks!

I just wanted to say thanks for both "Stitch" and "SeqPrep". They seem to be very useful !!
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