DEXSeq for exon counting & package name for human?

Question

[tinmad]

Hi,

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 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 exon 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, 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 (knocked down) with control. So I wonder what is the right package name for this case.

Answer 1

[Devon Ryan]

1. Yes, the DEXseq script is a wrapper around htseq-count that produces appropriate numbers. Use it rather than htseq-count
2. Your data is not in a package. See section 2.6 of the vignette for examples of loading data.

[tinmad]

Thank you for your help!
For the second question, then is it okay if I follow the same package with the vignette?
or Do I have to process any other alternative way?

[Devon Ryan]

I'm not sure what you mean by "follow the same package". If you mean follow DEXSeq's vignette, then yes you should do that. If you mean, "should I still load the pasilla package?", then no, that's just an example dataset. More specifically, you'll need to use the DEXSeqDataSetFromHTSeqCount() function.

[tinmad]

Sorry for the confusion, yes, it was about pasilla package!

About your specific comment, do you mean that I have to use DEXSeqDataSetFromHTSeq() function without loading any package? I'm just confused that what should I type instead of inDir = system.file("extdata", package="pasilla") from the vignette. If I don't need to load any package, do I have to type something like inDir = system.file("mysample")?

[Devon Ryan]

Yes, you MUST use DEXSeqDataSetFromHTSeq() to load your data. You will not use any system.file() commands, only DEXSeqDataSetFromHTSeq().