Question: Could Flicker (Illumina Mirna-Seq Analyzer Tool) Report Counts As Raw Counts Instead Hna (Normalized)?
2
gravatar for Pablo Marin-Garcia
8.2 years ago by
Spain
Pablo Marin-Garcia1.8k wrote:

flicker reports normalized hits (HNA) but tools like DESeq (http://www-huber.embl.de/users/anders/DESeq/) uses for their analysis raw data (from tables with integers).

When I look to the mir/xxx.hit.txt it looks like:

mir.fa/rno-let-7a       8975.83333333333        630.2373006394
mir.fa/rno-let-7a-1*    3       0.210644720295408
mir.fa/rno-let-7b       1908.83333333333        134.028554530184
mir.fa/rno-let-7b*      4       0.280859627060544
mir.fa/rno-let-7c       60.3333333333333        4.23629937482988
mir.fa/rno-let-7c-2*    3       0.210644720295408
mir.fa/rno-let-7d       571     40.0927117628927
mir.fa/rno-let-7d*      506     35.5287428231588
mir.fa/rno-let-7e       135     9.47901241329337
mir.fa/rno-let-7e*      1       0.070214906765136

Is there any place in the outputs of flicker where the number of possible mappings of a read is stored so I can turn the HNA into raw count? Or is there a way of running flicker again not having the multiple mapping normalized?

rna deseq mirna • 1.9k views
ADD COMMENTlink modified 8.2 years ago by Lars Juhl Jensen11k • written 8.2 years ago by Pablo Marin-Garcia1.8k

Thanks Lars for the tag editing.

ADD REPLYlink written 8.2 years ago by Pablo Marin-Garcia1.8k
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