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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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what is the expected mapping rate? #24

Closed bihuimel closed 5 years ago

bihuimel commented 5 years ago

Thanks for updating the tool. I am curious what the expected "percent mapped" should be for mouse tumor samples? I am getting anywhere from 2-4%, which seems quite low considering there are a lot of TEs in the genome. Is this expected or do I need to adjust any settings? Thanks!

hyunhwan-jeong commented 5 years ago

@bihuimel, If you are using RNA-Seq in your analysis, the mappability is normal range. RNA-Seq reads tend to be from exon regions, and a few of them are from intronic regions, which TE tend to be located. Therefore, you don't need to do any adjustment for your analysis.

Best Regards,

Hyun-Hwan Jeong