Sequencing Information from BAM file

Question

[MarVi]

Hello all!

Hope you are all doing well.

I have a tricky question, maybe someone of you will have some thoughts.

I would like to know if it is possible to get the following information from a Bam File.

a. stranded or un-stranded library?

b. In the case it is stranded: reads are paired-end or single-end?

c. In the case of paired-end: it is a Forward/Reverse of Reverse/Forward library?

In any case, I would like to have your advices if there is any in how to do have all this information easily!

Thank you in advance for your responses!

Have a nice day!

Answer 1

[GenoMax]

This should help address 2 perhaps all 3. RSeQC.

[MarVi]

This seems to do what I need!!

Thanks so much!