BAM files and RNA-seq protocols

[bogdan]

Dear all,

I have a BAm/SAM file generated from a RNA-seq samples and I am aiming to determine if the RNA-seq is PAIRED/UNPAIRED, or STRAND SPECIFIC. Please could you let me know which flags in the BAM/SAM files I shall check. Thanks a lot, and happy weekend,

-- bogdan

[rnaeye]

You can easily check directionality by the following tool
infer_experiment.py from http://rseqc.sourceforge.net/

bamtools stats command should tell you if you are paired o single end I believe. You need to install bamtools.