generate fastq with bed file

Question

[sacha]

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).

[Pierre Lindenbaum]

Please comment or mark as 'answered' your previous questions:

• How to get exon number from position from script?
• genome browser with genomic coordinate
• samtools : print single columns at position
• bcftools extract data

Answer 1

[sacha]

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

[endrebak]

That generates a fasta, not a fastq :)

[sacha]

fasta to fastq is easy !