From the docs of DESeq and forums seems to me that it is not a good idea to use data count that has been normalized by multiple mapping. My read counts has been produced with illumina's flicker that produce HNA (Hit Normalize Abundance), therfore not the right input for DESeq. Then I have to options:
a) use another tool for the DE that can use this type of counts. Any suggestion?
b) process again the sequended reads to obtain raw data. Do someone know how to tell Casava to do the mapping in a way that flicker gives raw data?. Would you suggest another pipeline for processing the miRNA that gives the right input for DESeq?
-Pablo
a) use another tool for the DE that can use this type of counts. Any suggestion?
b) process again the sequended reads to obtain raw data. Do someone know how to tell Casava to do the mapping in a way that flicker gives raw data?. Would you suggest another pipeline for processing the miRNA that gives the right input for DESeq?
-Pablo
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