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

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

rna-seq next-gen

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updated 4.0 years ago by Ram

• written 10.6 years ago by Bogdan

1 answer

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.

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written 10.6 years ago by Devon Ryan

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