Counting starting and ending positions of reads in reference genome

Question

[bobbyle0210]

Hi, Currently, I am working with NGS processing data. After getting SAM/BAM file, now, I want to output a text file that indicates the starting (5 end) and ending (3 end) position of each read in the corresponding reference sequence as well as the sequence of the read. The output file may look like:

---

ref_seq_1 starting_point read_1_sequence ending_point

---

ref_seq_1 starting_point read_2_sequence ending_point

---

ref_seq_2 starting_point read_3_sequence ending_point

---

I guess that I may need to use bedtools but I am still not sure which command should I use to obtain such information. Could you guys give me some suggestions? Thank you so much.

Answer 1

[Pierre Lindenbaum]

https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html