Forum:WGBS alignment with BitMapperBS

Question

[Shicheng Guo]

Now, it is time to try a faster WGBS alignment tool: BitMapperBS

./bitmapperBS --index human_genome.hg38.fa
trim_galore --paired read_1.fq read_2.fq
./bitmapperBS --search human_genome.hg38.fa --seq1 read1.fq --seq2 read2.fq  -t 6 --bam -o output.bam
MethylDackel extract reference_genome.fa alignments.bam

[Devon Ryan]

I have to admit being surprised by how fast bitmapperBS is. For those wondering you can install it via conda.

[sklages]

I love all these chinese comments spread all over the code ;-)

[hcheng]

I'm still adding some new features to bitmapperbs, so these chinese comments have not been removed ...

[hcheng]

Thank you a lot : ). Following your suggestions, I'm trying to make BitMapperBS calculate MAPQ like BWA, and then submit it back to PCB ..

[Devon Ryan]

Awesome!

[hcheng]

Thank you for your poster. I just worry about how to publish BitMapperBS ...

[Shicheng Guo]

Nature Protocol? Nature Method? Nucleic Acid Research? You can suggest Devon Ryan as one of the preferred reviewers.

[hcheng]

It had been rejected by several reviewers. Some of them said they didn't think BitMapperBS is better than existing methods, some other people said it is lack of novelty, and some others said bs-seq aligner is not important ... Now I just want to publish it.

[Shicheng Guo]

Maybe you didn't suggest the best reviewers. Sure. different people have different comments to same tools. You need to find some experts who appreciate your tools.

[hcheng]

Thank you so much! You know in most cases editors do not use the reviewers recommended by the authors, and some editors may directly reject submission without big name. Good luck to me ...