Question: Counting starting and ending positions of reads in reference genome
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gravatar for bobbyle0210
12 days ago by
bobbyle02100 wrote:

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.

rna-seq sam bam ngs bedtools • 95 views
ADD COMMENTlink modified 12 days ago by Pierre Lindenbaum123k • written 12 days ago by bobbyle02100
0
gravatar for Pierre Lindenbaum
12 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

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

ADD COMMENTlink written 12 days ago by Pierre Lindenbaum123k
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