RNA-seq data annotation

[tamari]

Hi,

I have an alingment of PE reads (100bp) from RNA-seq (BAM file) and I would like to know what is the best way to estimate the percantege of the genomic features in the library that were aligned, i.e exon, intron, 5UTR, 3UTR etc... as well as types of RNAs like coding, non-coding ( miRNA, lincRNA ,tRNA/rRNA...)

I know that there is something in bedtools package (perhaps intersect or coverage) but I am not sure how to use it in the best way so I get the most accurate picture because I expect overlaps between different features.

I tried to look for something simillar in R (bioconductor ) but I can't find anything.

I would really appreciate your help,

Tamari

[Bukowski]

http://picard.sourceforge.net/comman...tRnaSeqMetrics

[pbluescript]

This software can do many of the things you want:

https://code.google.com/p/rseqc/

If you want to get really specific about the types of RNA that are represented in your sample, then using something like bedtools intersect with custom GTF files would be useful.

[tamari]

Thanks for your help!