SAM file and RNA-seq stranded/unstranded paired/unpaired

Question

[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

Answer 1

[Devon Ryan]

Flag 1 will tell you if any of the reads are paired-end. Strand-specificity of the library prep isn't stored in SAM files, but RNA-SeQC can infer this for you.