BWA with multi read files

[thh32]

Hi I have never used BWA before and so was wondering if anyone knows how I can use BWA to map my reads to my reference genome. My data is as follows:

L001_R1.fasta
L001_R2.fasta
L002_R1.fasta
L002_R2.fasta
etc
There are 12 files in total and as you can see they are paired reads.
So does anyone have any idea?
Any help would be much appreciated.

Thanks,
Tom

[thh32]

Also I have indexed my referance genomes (I have 93 genomes together in a single fasta) and been provided with 5 files : Combined_genomes_index_bwa.amb Combined_genomes_index_bwa.ann Combined_genomes_index_bwa.bwt Combined_genomes_index_bwa.pac Combined_genomes_index_bwa.sa

How do I use these for my mapping as I want to use bwa mem as the reads length range from 40 to 140 but the manual doesnt state how to input these index files

bwa mem [-aCHMpP] [-t nThreads] [-k minSeedLen] [-w bandWidth] [-d zDropoff] [-r seedSplitRatio] [-c maxOcc] [-A matchScore] [-B mmPenalty] [-O gapOpenPen] [-E gapExtPen] [-L clipPen] [-U unpairPen] [-R RGline] [-v verboseLevel] db.prefix reads.fq [mates.fq]

Again, any help would be great.

[bruce01]

From the manual:

bwa mem ref.fa read1.fq read2.fq > aln-pe.sam

Just make sure your fasta file is in the same dir as your index files and there shouldn't be any problems.

As to your first question, I presume the above command shows how to use PE data?

[mastal]

Use the base name of the index files as 'db.prefix', so you would use
'Combined_genomes_index_bwa' as the name of the index (and provide the complete path to the index files if necessary).

The online manual doesn't seem to specify what to do if your reads are in more than 1 file. Try listing all the R1 files separated by commas but no spaces, followed by the R2 files, again separated by commas but no spaces.

 L1_R1.fastq,L2_R1.fastq,L3_R1.fastq... L1_R2.fastq,L2_R2.fastq,L3_R2.fastq...

If that doesn't work you could combine all your R1 files together and all your R2 files.

[thh32]

bruce01, I have tried your method and it just didnt work at all, no error message just a list of the commands.Will try the method you suggest mastal now.

[thh32]

Right using mastal's method this error occured [E::main_mem] fail to open file ' LIST OF ALL FILES'

It appears to be that if I leave spaces between the files it just ignores the whole thing and provides a list of the commands however if I remove the space and put commas then it see's it as one long file name which it cannot locate.

[bruce01]

OK, can you tell me the exact command you used, and whether you want to align all your fastq at the same time (ie L001+L002+...+L00n), or individually (ie L001 makes single SAM file)?