Question: SAM file and RNA-seq stranded/unstranded paired/unpaired
0
gravatar for Bogdan
3.4 years ago by
Bogdan750
Palo Alto, CA, USA
Bogdan750 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 • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Devon Ryan90k • written 3.4 years ago by Bogdan750
0
gravatar for Devon Ryan
3.4 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k 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 3.4 years ago by Devon Ryan90k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1180 users visited in the last hour