Question: generate fastq with bed file
0
gravatar for sacha
2.4 years ago by
sacha820
France
sacha820 wrote:

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

generator fastq bed • 1.2k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by sacha820

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

ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum101k
1
gravatar for sacha
2.4 years ago by
sacha820
France
sacha820 wrote:

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 
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by sacha820

That generates a fasta, not a fastq :)

ADD REPLYlink written 7 months ago by endrebak570

fasta to fastq is easy !

ADD REPLYlink written 7 months ago by sacha820
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