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Can I bulid a new reference for bwa ?

Hi, I wanna use a specified gene sequence to build a reference , and then mapp PE fastq files (fq1,fq2) to this new reference gene genome via BWA .

that's just a thought ,I do not konw it's availble ? if availble, which algorthims should I choose from BWA ??

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genome alignment gene
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updated by alons alons • written by winter_li • winter_li

2 answers

HI winter_li, Here's how you can create a custom reference genome:

  1. Make a tab delimited CSV file where the first column is chr<chromosome number=""> (chr6 for example), the second is the start position and third is the end position.

  2. Rename as .bed file.

  3. Use BED tools with the following command:

bedtools getfasta -fi (complete reference fasta file).fa -bed (bed file).bed -fo (custom reference fasta file).fa.out

  • ^ You can leave out the .out.

FInally, you index the new file using bwa.

• 1 views • link
written by alons alons

You're welcome! if it worked out for you, please consider accepting my answer by pressing the "V" (accept) button next to my post, it might help others in the future to easily find the solution they were looking for. Good luck!

• 2 views • link
written by alons alons

Read the Manual - First Command in the synopsis is building an index.

• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Hi, I mean I do not use the complete human genome as a reference ,I use a gene sequence as a reference ,It's available ?

• 1 views • link
written by winter_li • winter_li

Yes, that's fine too.

• 1 views • link
written by mastal511 mastal511

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