Region "Awk" Specifies An Unknown Reference Name
Hello, can you look at what is wrong by using samtools command?
#!bin/bash
samtools view -o raw_genome.txt my.bam awk '{print $3, $4, $10;}' \
raw_genome.txt >raw_sequence.txt
What I got is
[main_samview] region "awk" specifies an unknown reference name. Continue anyway.
[mainsamview] region "{print $3, $4, $10;}" specifies an unknown reference name. Continue anyway. [mainsamview] region "raw_genome.txt" specifies an unknown reference name. Continue anyway.
Thanks
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1 answer
Add a pipe "|" and remove the -o option and do something like that:
samtools view my.bam | awk '{print $3, $4, $10;}' > Raw_File.txt
The pipe will redirect the output of your first command to the next command
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