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).
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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
That generates a fasta, not a fastq :)
fasta to fastq is easy !
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