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): ********************************************** 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
Roberts Lab 