Question: SAM file and RNA-seq stranded/unstranded paired/unpaired
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gravatar for Bogdan
3.9 years ago by
Bogdan890
Palo Alto, CA, USA
Bogdan890 wrote:

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 • 1.3k views
ADD COMMENTlink modified 3.9 years ago by Devon Ryan93k • written 3.9 years ago by Bogdan890
0
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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.

ADD COMMENTlink written 3.9 years ago by Devon Ryan93k
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