Question: Convert fastqc.gz file to BED file format
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gravatar for ss20g16
4 months ago by
ss20g160
ss20g160 wrote:

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

fastqc rna-seq chip-seq bed • 224 views
ADD COMMENTlink modified 4 months ago by GenoMax95k • written 4 months ago by ss20g160

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

ADD REPLYlink modified 4 months ago • written 4 months ago by Medhat8.8k

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.

ADD REPLYlink modified 4 months ago • written 4 months ago by ben.kunfang30
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