Steven generated destranded (“merged”) coverage files from Bismark .cov output.
Files are here: https://osf.io/yem8n/files/ under “bismark_coverage_files” under “merged_tab”.
I believe Steven did this using this notebook:
40-cov2cyt-zero.ipynb
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221th Post
x journal post for Pt. Whitney x repo releases x improve organization x create readme Geoduck paper BS pipeline destranded 5x coverage files: convert to allc format (chr start update results reimbursements talk with steven about xpt whitney next week, how I’m doing and plans, SLO job? proteomics continue edits...
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Thur. Dec. 19, Geoduck Brood Conditioning
Broodstock Experimental Setup
New algae feeding system
Matt set up a new algae feeing system!
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Wed. Dec. 18, Oyster paper stats
PCA of all data show grouping of samples from different temperatures with subsequent time points. This seems to indicate an interaction effect of time x temperature
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Tues. Dec. 17, DMR pipeline
STEP 1: Bismark alignments
A. Build bismark genome
B. Align FASTQs
C. Sort bam files
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