Convert fastqc.gz file to BED file format
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13 months ago
ss20g16 • 0

How would I convert a file that is fq.gz (fastq.gz) to BED file format? I'm working on the Iridis command line (MobaXterm; Linux command line) - what code can I use to achieve this? thanks

RNA-Seq ChIP-Seq fastqc BED • 545 views
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May I ask why you are doing that? (by the way, do you mean fastq.gz?).

You can get something like:
Sequence_name\t0\tlength_of_read

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You should use bowtie2 or bwa to map fq.gz to some reference genome (human:hg38/hg19) first to get the sam file and use bedtools to convert sam file to bed file.

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