convert bam to fastq sequence based on the special region.
2 answers
Extract a sub-bam with
samtools view -b -o out.bam in.bam Chr01:2000-50000
and extract the fastqs with SamToFastq (using option UNPAIRED_FASTQ)
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by
Ram
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written
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Pierre Lindenbaum
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written
by
Pierre Lindenbaum
You can do everything with samtools (bam needs to be indexed with samtools index file.bam):
samtools view -h file.bam Chr01:2000-50000 | samtools bam2fq - > file.fastq
Splitting single reads and paired reads to different files:
samtools view -h file.bam Chr01:2000-50000 | samtools bam2fq -s file-se.fastq - > file-pe.fastq
Or compressing the fastq:
samtools view -h file.bam Chr01:2000-50000 | samtools bam2fq - | gzip > file.fastq
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