Originally posted by emilyjia2000
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for exon counting i have reverted to using there supplied script within the dexseq package (dexseq_count.py) which depends on htseq.
i assume you already have the package and used one script to write the flattened gff file. the scripts are located in:
DEXSeq/inst/python_scripts
the options are outlined in the script and account for paired-end reads, strandedness, and quality.
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