extract region from the bam file
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3.1 years ago
9521ljh ▴ 50

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.

assembly sequencing genome • 998 views
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.bed *.bam

These are your actual filenames?

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Beside WouterDeCoster 's question: How have you checked the output?

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Yes. the output just enumerate All NNNNNNNNNNNNNNNNNNNNNNN

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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.

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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.

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