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.

see https://github.com/RobertsLab/resources/issues/860

@sr320 newly trimmed reads are on mox here:
/gscratch/scrubbed/strigg/analyses/20200319

reads with specified adapters trimmed:

/gscratch/scrubbed/strigg/analyses/20200319/specify_a/EPI-167_S10_L002_R1_001_val_1.fq.gz
/gscratch/scrubbed/strigg/analyses/20200319/specify_a/EPI-167_S10_L002_R2_001_val_2.fq.gz


reads with TrimGalore! defaults adapter trimmed:

/gscratch/scrubbed/strigg/analyses/20200319/EPI-167_S10_L002_R1_001_val_1.fq.gz
/gscratch/scrubbed/strigg/analyses/20200319/EPI-167_S10_L002_R2_001_val_2.fq.gz
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.

https://d.pr/n/i4IacO

https://d.pr/n/WJjSh8

Bismark Reports

specified adapters
deduplicated

https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/031920-trimtest/sa/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.html

non-deduplicated

https://gannet.fish.washington.edu/tmp/031920-trimtest-nod/sa/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.html

TG default
deduplicated

https://gannet.fish.washington.edu/tmp/031920-trimtest/tgd/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.html

non-deduplicated

https://gannet.fish.washington.edu/tmp/031920-trimtest-nod/tgd/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.html

Video Wrap up - https://washington.zoom.us/rec/play/7p0qJbyuq283HoKT5QSDUPcqW428f6ys03Ub-_ZezEqwUHcDMFH3MONBY5AMORmk5MWjwa73E94RvG4?continueMode=true