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.
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BAM files and RNA-seq protocols
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
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