Question: What is default paprameter of BWA mem mapping
0
gravatar for Bioinfonext
3.2 years ago by
Bioinfonext200
Korea
Bioinfonext200 wrote:

Please Discuss the default parameter setting of BWA mem.

I used bbmap and BWA mem with default setting to map raw reads to CDS transcripts and I found that BWA is able to map more number of reads in comparison to bbmap.

I know in bbmap default setting is 76% identity but not aware about BWA mem.

Thanks

rna-seq • 3.5k views
ADD COMMENTlink modified 3.2 years ago by Jenez520 • written 3.2 years ago by Bioinfonext200
1

By default, BWA produces multiple alignments per read, while BBMap does not unless you add the "ambig=all" flag. Be sure that you are counting correctly - the number of alignments produced is not the same as the number of reads that map. The difference is particularly large for transcriptome mapping because of all the duplication due to isoforms.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Brian Bushnell17k
2
gravatar for vmicrobio
3.2 years ago by
vmicrobio240
vmicrobio240 wrote:

Default seed is 19 bp, you can change it with '-k' option

bwa mem -k 30 reference.fasta file.fastq > alignment.sam

seed will be now 30 bp

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by vmicrobio240
2
gravatar for Jenez
3.2 years ago by
Jenez520
Sweden
Jenez520 wrote:

I would take a guess and say that the default settings for each parameter can be found on the documentation page for bwa mem here.

See the values within [ ] for the default parameters.

ADD COMMENTlink written 3.2 years ago by Jenez520
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