Question: DEXSeq for exon counting & package name for human?
0
gravatar for tinmad
3.2 years ago by
tinmad10
Korea, Republic Of
tinmad10 wrote:

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 (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.
  

rna-seq counting exon dexseq • 1.3k views
ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 3.2 years ago by tinmad10
2
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:
  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.
ADD COMMENTlink written 3.2 years ago by Devon Ryan88k

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?

ADD REPLYlink written 3.2 years ago by tinmad10

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.

ADD REPLYlink written 3.2 years ago by Devon Ryan88k

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 vignett. If I don't need to load any package, do I have to type something like inDir = system.file("mysample") ?

ADD REPLYlink written 3.2 years ago by tinmad10

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

ADD REPLYlink written 3.2 years ago by Devon Ryan88k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1061 users visited in the last hour