Question: Using BWA Index and i get 5 output files, but BWA-mem asks for just 1
0
gravatar for SaltedPork
2.6 years ago by
SaltedPork90
SaltedPork90 wrote:

I'm using 1000 genomes pilot data, I've downloaded 3 zipped files. And I then use all three in the same command so it looks like this:

bwa index input_1.fastq input_2.fastq input_3.fastq

This produces 5 files, 2 are binary and 3 are fastq again.

But the usage for BWA-mem asks that the index be specified as 1 file, what's going on here? thanks!

bwa bwa-index • 4.1k views
ADD COMMENTlink modified 8 months ago by mirzaabid0 • written 2.6 years ago by SaltedPork90

Hi, I was working to make an index file for bacterial genomes by using BWA command

bwa index -a bwtsw bacterial_genomes.fna

This command was working from last 4 days and was functional due to big database, suddenly due to power outage this command was interrupted. I want to continue this command from last point where it was working before power outage. Please help me regarding this issue.

ADD REPLYlink written 8 months ago by mirzaabid0

No you can't do that. You have to start over. There is no way around this.

ADD REPLYlink written 8 months ago by genomax66k
3
gravatar for genomax
2.6 years ago by
genomax66k
United States
genomax66k wrote:

One does not index fastq files. One would index the genome fasta that you want to search against using the fastq files.

Is that what are you trying to do?

ADD COMMENTlink written 2.6 years ago by genomax66k

I think so, when you say genome, are you referring to the human genome reference file. I have some 454 data, and a file with LINE-1 transduction data so I'm trying to in simple terms, find all the transduction sites in the 454 data, hence why i thought i would need to index that.

ADD REPLYlink written 2.6 years ago by SaltedPork90

A reference can be any fasta sequence. You would index that fasta file and then map your reads against that index. What format is LINE-1 transduction in? Is it a fasta file?

ADD REPLYlink written 2.6 years ago by genomax66k

its in fasta. When specifying the reference file in the bwa-mem command, do i use the original fasta, or the newly created 5 files?

ADD REPLYlink written 2.6 years ago by SaltedPork90
1

You will index first.

bwa index -p index_base my_fasta.fa

Then do bwa mem using the "basename" of the index files (which in this case would be index_base, use some other name that you like)

bwa mem [options] index_base file1.fastq
ADD REPLYlink written 2.6 years ago by genomax66k
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