I've assembled a metagenome using MEGAHIT and begun testing different mapping options to perform the binning of the contigs. However, I've noticed that Bowtie2 and BWA-MEM had very different mapping rates to the metagenome:
Bowtie2:
182783328 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
55100932 + 0 mapped (30.15% : N/A)
182783328 + 0 paired in sequencing
91391664 + 0 read1
91391664 + 0 read2
46385654 + 0 properly paired (25.38% : N/A)
49135024 + 0 with itself and mate mapped
5965908 + 0 singletons (3.26% : N/A)
2364578 + 0 with mate mapped to a different chr
1755482 + 0 with mate mapped to a different chr (mapQ>=5)
BWA-MEM:
184716120 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
1932792 + 0 supplementary
0 + 0 duplicates
116629821 + 0 mapped (63.14% : N/A)
182783328 + 0 paired in sequencing
91391664 + 0 read1
91391664 + 0 read2
93117324 + 0 properly paired (50.94% : N/A)
107719404 + 0 with itself and mate mapped
6977625 + 0 singletons (3.82% : N/A)
14496150 + 0 with mate mapped to a different chr
11129016 + 0 with mate mapped to a different chr (mapQ>=5)
BWA-MEM mapped way more reads than Bowtie2. As the metagenome was assembled using those reads, I think that Bowtie2 mapping only 30% of them is quite strange.
What may be causing this difference? As the .bam file will be used for binning, using the output of one tool or the other will greatly affect downstream analysis.
Thanks!
Can you post the bowtie2 and bwa commands used?
Sure! They were both executed with the default parameters.
This might be an ignorant question, but why assemble before you map? Are the two not mutually exclusive?
Because I didn't have a metagenome to map to :)