generate fastq with bed file

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

• 5,268 views • link

updated 3.7 years ago by Ram

• written 11.1 years ago by sacha

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

• 0 views • link

updated 3.7 years ago by Ram

• written 11.1 years ago by Pierre Lindenbaum

1 answer

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

• 0 views • link

updated 6.8 years ago by Ram

• written 11.1 years ago by sacha

That generates a fasta, not a fastq :)

• 0 views • link

written 9.3 years ago by endrebak

fasta to fastq is easy !

• 0 views • link

written 9.3 years ago by sacha

More posts like this

Exome capture file from ensembl
written 4.5 years ago by mailard •

Hello! I need an interval list and bed file for exome analysis (example https://www.twistbioscience.com/resources/bed-file/ngs-human-core-exome-panel-bed-files) but from Ensembl. How can do an interval list for WES …
Is there any script on how to check the depth of the sequencing region on my Mac terminal?
written 5.7 years ago by nudrylab •

Hello, I am trying to find a script that can help me check the depth of sequencing of the region. I want to see if …
Extracting only reads mapped to specific genomic region
written 5.7 years ago by agata •

I have a specific genomic region saved as `fasta`. I want to check how many reads mapped to this specific region and extract them, as …
Call alternative base for each position in a bam file
written 6.1 years ago by sacha

Hi, From a bam file and a target bed file, I would like to extract each base count. I don't want to skip low frequency …
Generate artificial reads
written 8.6 years ago by finswimmer

Hello, i need to generate some artifical reads. `randomsreads.sh` from BBMap seems to be the right program for me. I don't need random reads for …
How to transfer annotation from HG19 to genome sequence.
written 8.9 years ago by clear.choi •

If I have example genome sequence (3GB) around 4000 contig. And maximum contig length is 15Mbp. Also, I have bed file for HG19. Could someone …
Agilent focused exome panel public example fastq data
written 9.3 years ago by abdulbenissa •

Hello, Everyone !! I was looking for a source to obtain FASTq files for the panel focused exome panel from agilent. I had to use …
Creating alternate Bed file by incorporating INDELs locations
written 10.9 years ago by ersgupta •

I have a exome bed file (coordinates wrt to ref genome) and a bed file with coordinates of INDELs (incorporated in ref genome). Now I …
Where To Get The Annotation File For The Nimblegen Seqcap Ez Exome V1
written 13.2 years ago by ewre

<p>Hi, everyone I have got 10 exomes data the capture technology use by which is NimbleGen SeqCap EZ exome V1, but I found that NimbleGen's …
Can Ncbi Blast Only Search A Special Region In Database For Hits?
written 13.8 years ago by litiancheng.gansu •

<p>I want to blast my 36SE reads to a special region of HG19, does NCBI BLAST can do this special region search? If so, how …