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Old 09-14-2009, 01:43 PM   #1
bioinfosm
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Default mRNA seq 75bp splice file

Illumina provides a human.49.splice ELAND_RNA_GENOME_SPLICE file for 50bp reads. Does someone have the same file for 75bp reads?

There is this thought that 75bp reads are too long for mrna-seq, as they may cover more than one splice sites, thus causing more harm than help. Do people have comments on that? We have 75 bp reads and wish to use the Illumina Genome Studio pipeline but do not have access to the 75bp splice file.

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Old 09-20-2009, 05:29 PM   #2
joseph
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use TopHat, it breaks the 75 bp read into 3 segments. I heard TopHat does this to prevent the problem you mentionned, but I am not sure!
I hope Cole comments on this!
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Old 09-30-2009, 07:42 PM   #3
kch
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I'm also wondering about how TopHat handles these smaller segments. If the segment spans across a splice junction, can Bowtie align this or is this information lost?

Update: just re-read the paper and it explains how it works quite nicely

Last edited by kch; 09-30-2009 at 08:13 PM. Reason: answered my own question
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Old 11-23-2009, 09:19 PM   #4
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One of the perl scripts that comes with the pipeline software can be used to generate splice junction indexes of any size you'd like.
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Old 11-30-2009, 07:16 AM   #5
bioinfosm
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Quote:
Originally Posted by graveley View Post
One of the perl scripts that comes with the pipeline software can be used to generate splice junction indexes of any size you'd like.
Could you give the name of that script?
thanks
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