Can I bulid a new reference for bwa ?
2
0
Entering edit mode
8.3 years ago
winter_li ▴ 60

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 ??

BEST

genome alignment gene • 3.6k views
ADD COMMENT
1
Entering edit mode
8.3 years ago
alons ▴ 270

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.

ADD COMMENT
1
Entering edit mode

got it ,thank you !

ADD REPLY
0
Entering edit mode

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!

ADD REPLY
2
Entering edit mode
8.3 years ago

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

ADD COMMENT
0
Entering edit mode

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 ?

ADD REPLY
0
Entering edit mode

Yes, that's fine too.

ADD REPLY

Login before adding your answer.

Traffic: 2747 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6