For Duck Sake

Going back to take a peek to see what treating geoduck EPI data as WGBS will look like.

Shelly trimmed up some data and I ran it through Bismark.


@sr320 newly trimmed reads are on mox here:

reads with specified adapters trimmed:


reads with TrimGalore! defaults adapter trimmed:

Can you:

align these reads with Bismark to the OFS genome 'Panopea-generosa-v1.0.fa' (I have a bismark genome for this here: /gscratch/srlab/strigg/data/Pgenr/OFS )

Deduplicate aligned reads

Run bismark methylation extractor on deduplicated alignments and non-deduplicated alignments

Sort and index resulting bams for viewing in IGV

Set up two jobs, one with deduplication, one without.

Bismark Reports

specified adapters


TG default


Video Wrap up -

Written on March 20, 2020