I want to get exon count so I tried HTSeq-count first (with exon_id option)
but I found that DEXSeq is better for this purpose.
I followed the manual (http://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf)
and got a result of reads counting as a *.txt file by running the script python_count.py.
So my questions are,
1) If I want to get excon counts only, is it a right approach?
(is the txt file from python_count.py the final output for this case?)
2) In the manual (http://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf),
they used the pasilla dataset so they used the package pasilla (p6 of the manual).
However, my samples are about human and I want to compare test(knockdowned) with control.
So I wonder what is the right package name for this case.