Question: Why does total unique map not equal to library size?
gravatar for Ahdee
4 months ago by
United States
Ahdee40 wrote:

Hi I'm using Star align and the build in htseq to count gene features. 

however I notice that the final log file, specifically "Uniquely mapped" does not matched the total library size of the count. For example, I could have  sample where the uniquely mapped is 63 million but the the total library size, that is the sum of all the gene count is 54 million? So my question is what is going on here since I though part of the count was to categorized the counts into each gene  so that the sum should be equal? 


thank you. 


ADD COMMENTlink written 4 months ago by Ahdee40

Neither STAR nor HTSeq are Bioconductor software. Biostars is a more relevant forum.

ADD REPLYlink written 4 months ago by Dario Strbenac1.4k

Can you post the full log, please?  Also point out where what particular line in the log has the unexpected number.

ADD REPLYlink written 4 months ago by Pariksheet Nanda70
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