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Old 04-11-2013, 06:59 AM   #1
kanewong
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Default How to trim RNA-seq file and compare splice-junction tools results

Hi all,

I am a newbie to bioinformatics and this forum. Hopefully I am posting my question in a proper way.

I am currently running tophat, splicemap and mapsplice on a set of RNA-seq data, I would like to know the following matters:

1. Is there any easy-to-use tools to trim a RNA-seq file into a shorter read-length one? I made a search on the internet and found that perl seems to be one of the solution. Since I haven't learned perl before, I wonder if there are any other tools which are easier to use.

2. After running the splice-junction tools, I want to compare the overlap of their results. I made a search and a webiste suggests I can use Rsamtools and GenomicRanges
packages of R software to do so. Is it an easy and common way to compare splice-junction tools results?

As long as the tool is easy to use, it is fine for me.

Thank you very much
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