generate fastq with bed file
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9.3 years ago
sacha ★ 2.4k

I want to generate fastq file for testing.. I already check FastQArtificialGenerator, wsgim and Simseq. But it seems I cannot specify a region from a bed file.

For example, from hg19, I only want a fastq where reads map my bed file (exome).

fastq bed • 4.6k views
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9.3 years ago
sacha ★ 2.4k

I solve it ..

I just need to create a new reference containing my bed coordinate!

bedtools getfasta -fi ref.fa -bed target.bed -fo newref.fa
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That generates a fasta, not a fastq :)

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fasta to fastq is easy !

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