quality management

[christinawu2008]

Hi All,

I want to ask if I do different trimming for different datasets (some kept 50bp, some are with 80bp left). does it influence DE analysis?

Christina

[seb567]

Hello,

I believe that digital expression analyses are based on a metric called RPKM, short for
Reads Per Kilobase of exon model per Million mapped reads. Trimming your reads will not change the total number of reads unless you trim any read entirely.

However, trimming reads will change the alignments, presumably.

Therefore, it will change the number of Reads Per Kilobase of exon model per Million mapped reads, thus changing the digital expression.


Sébastien

Hi All,

I want to ask if I do different trimming for different datasets (some kept 50bp, some are with 80bp left). does it influence DE analysis?

Christina