[BioC] problems running DEXseq

[Steve Lianoglou]

Hi Diya,

Please use "reply all" when responding to mails from this list so that discussion stays "on line" and is visible by more people.

This way you will likely get better help, and we can also use these lists as a source of help for other people who are doing similar things.

That having been said:

> Thanks for your response and the PDF file.. It really helps. I have aligned fastq reads to UCSC hg 19 genome.in that case how can I use the genomic ranges for UCSC specific genome.. ?

You would use a GenomicFeatures::TranscriptDb object built from gene annotations against hg19. This pre-compiled one would be a good place to start:

http://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html

Which I believe was compiled from the UCSC knownGene table:

https://genome.ucsc.edu/FAQ/FAQdownloads.html#download31

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech