How to handle DNA methylation duplication in Bismark?

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6.9 years ago

ahmad mousavi ▴ 800

Hi

I have run Bismark for RRBS data, but I think it is not fix duplicates problem.

Anybody know how to correct duplicates problem for Bismark aligner?

I found deduplicate_bismark_alignment_output.pl which works as a post alignment step for DNA methylation analysis in Bismark pipeline.

Thanks

sequencing alignment • 3.2k views

ADD COMMENT • link updated 4.2 years ago by Biostar 20 • written 6.9 years ago by ahmad mousavi ▴ 800

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You mean PCR duplicates? You can find them with picard.

ADD REPLY • link 6.9 years ago by Devon Ryan 104k

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You can also use clumpify (A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files ) to identify various duplicated without doing alignments.

ADD REPLY • link 6.9 years ago by GenoMax 147k

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In the documentation it is stated:

deduplicate_bismark --bam [options] <filenames>

"This command will deduplicate the Bismark alignment BAM file and remove all reads but one which align to the the very same position and in the same orientation. This step is recommended for whole-genome bisulfite samples, but should not be used for reduced representation libraries such as RRBS, amplicon or target enrichment libraries."

ADD REPLY • link 4.2 years ago by asumani ▴ 70

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