Hey there,
I have a co-assembly (assembled from 3 sets of PE reads) and would like to recruit all 3 read sets to the co-assembly at the same time. Is this type of mapping possible with BBMap? If so, how do you format the bbmap command?
Many thanks in advance!
Rebecca
You could use bbwrap.sh if you don't want to cat the inputs.
$ bbwrap.sh
Last modified April 21, 2015
Description: Wrapper for BBMap to allow multiple input and output files for the same reference.
To index: bbwrap.sh ref=<reference fasta>
To map: bbwrap.sh in=<file,file,...> out=<file,file,...>
To map without an index: bbwrap.sh ref=<reference fasta> in=<file,file,...> out=<file,file,...> nodisk
To map pairs and singletons and output them into the same file:
bbwrap.sh in1=read1.fq,singleton.fq in2=read2.fq,null out=mapped.sam append
Other Parameters:
in=<file,file> Input sequences to map.
mapper=bbmap Select mapper. May be BBMap, BBMapPacBio,
or BBMapPacBioSkimmer.
append=f Append to files rather than overwriting them.
If append is enabled, and there is exactly one output file,
all output will be written to that file.
What do you mean by
Are you referring to aligning your reads to an assembly made from these 3 sets of reads? While BBMap has some programs (e.g.
tadpole.sh) that can do k-mer based assembly it is mainly an alignment program. You could simplycatthe three sets of files together and align against the reference.Hello,
Exactly, the co-assembly was assembled from a combination of these 3 read sets. What I'm looking to do is align the 3 read sets to the co-assembled contigs - I was hoping there'd be an option in BBMap for handling multiple read sets. But if there isn't, I think your solution of using
catcould work, I'll check it out, thanks!