extract region from the bam file
i have sorted *.bam file and i want to extract particular regions mapping
i have .bed file
chr2 179390716 179695529
chr3 89825161 90460254
chr8 144939497 144952632
samtools view -b -L .bed *.bam > output
the output file have only NNNNNNNN, there's no reads. what is the problem? i already check if there position have reads or not.
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.bed *.bamThese are your actual filenames?
Beside WouterDeCoster 's question: How have you checked the output?
Yes. the output just enumerate All NNNNNNNNNNNNNNNNNNNNNNN
I have asked for the command you used for checking the content and not how the content looks like :)
Also, please answer the question by Wouter.
And another question: how did you get this bam file?
You'll need to share more information, we cannot guess what happened and cannot see your screen.