Sean’s Notebook: BWA-Meth Output for…

Sean’s Notebook: BWA-Meth Output for EPI-135.

Found a different methylation aligner, BWA-meth, that’s based on a Burrows Wheeler aligner that’s supposed to deal better with gap alignment than Bowtie2. Fired it up with the EPI-135 and 10k Geoduck genome. It gave an answer, but I *really* don’t believe it. The bamtools stats output I believe claimed 80% mapping rate. Compared to the 6% from Bismark.

sean@emu:~/Documents/Geoduck_Rerun/bwatest$ bamtools stats -in bwa-meth.bam

**********************************************
Stats for BAM file(s): 
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Total reads:       55253237
Mapped reads:      48098666	(87.0513%)
Forward strand:    30884874	(55.8969%)
Reverse strand:    24368363	(44.1031%)
Failed QC:         16970759	(30.7145%)
Duplicates:        0	(0%)
Paired-end reads:  55253237	(100%)
'Proper-pairs':    30054258	(54.3937%)
Both pairs mapped: 47463686	(85.9021%)
Read 1:            27626448
Read 2:            27626789
Singletons:        634980	(1.14922%)

.bam file is available: here

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