Question: Hg19 Acceptable Map Percentage
gravatar for yrc0313
4.7 years ago by
Brigham and Women's
yrc03130 wrote:

Hi everyone,

I'm new to RNA-seq and was wondering if there is a generally accepted minimum mapped percent (hg19)? Right now I seem to be getting around 60-70%. Thank you!

rna-seq • 743 views
ADD COMMENTlink written 4.7 years ago by yrc03130

Where is your sample coming from? Is there a possibility of contamination? If yes, from which source.

ADD REPLYlink written 4.7 years ago by Biomonika (Noolean)3.1k

The samples are from patients and were checked for contamination with none found. Thank you for your help!

ADD REPLYlink written 4.7 years ago by yrc03130

While the percentage can be much higher you have what you have. Are you using a splice-aware aligner? You can take a look at the reads that did not map by checking a few with blast @NCBI (unless you have already done this by "were checked for contamination").

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by GenoMax95k
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