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Old 05-20-2014, 07:17 AM   #1
Greenhorn
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Default Exclude short Reads?

Hi,

I read some guidelines for RNA Seq and I am wondering why people discard reads under a certain threshold of bp and then only take reads into account which map unique. Even if no assembly or so is done.

Isnīt this somehow redundant? I mean, if a read has a length, which is sufficient to find a unique position, why should i discard it? I "only" want to map the reads to an annotaded genome to find DGE...

Thanks in advance
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Old 05-20-2014, 09:37 AM   #2
dpryan
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If a read is too short then you don't bother mapping it. One doesn't normally map reads and then discard according to length for the reasons you noted.
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