Originally posted by Simon Anders
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Forgive my naivety, If multi-mapping becomes an issue when we are translating mapping reads to count data (expression level)...what than would be an acceptable standard to extract count data?? (is it using htseq-count ,bedtools, cuffdiff)
Also....during the mapping stage..what bias would be introduced, if we discard multimap reads?
Edit - you are correct in saying that the reads at location 2 is multimapped, many thanks for the insight!
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