Methylation analysis: P. generosa juvenile OA response

bismark currently running on full data set

mapping and coverage analysis with subsetted samples (10K reads each)

bismark summary
- all samples have > 50% mapping efficiency with Bismark settings –score_min L,0,-1.2 -I 60 –non_directional
- deduplication removed very few reads, per usual
- % methylation is on average 20%

methylkit summary - coverage plots don’t appear to obviously show any particular sample or condition should be excluded due to low coverage.this may become more obvious in the full analysis or downstream analysis
- the genome region > 60000 seems to have low coverage in all samples
plot of genome regions with no coverage organized by length of treatment

C. virginica

bismark run completed on mox

- last part failed because I copied from jupyter notebook and had '!' in the code still
- need to edit this part for future scripts, but for now i will complete the analysis on ostrich in my jupyter notebook
	- generate summary file
	- generate sorted bam files for methylkit analysis
- need to rsync everything onto Metacarcinus from Mox gscratch

failed code

	/var/spool/slurm/d/job394229/slurm_script: line 47: !cat: command not found
	/var/spool/slurm/d/job394229/slurm_script: line 51: !sed: command not found
	/var/spool/slurm/d/job394229/slurm_script: line 56: fg: no job control
	xargs: samtools: No such file or directory
	/var/spool/slurm/d/job394229/slurm_script: line 61: -o: command not found

code excerpt

	46 #create summary report
	47 !cat /gscratch/srlab/strigg/analyses/20181004/*PE_report.txt | \
	48 grep 'Mapping\ efficiency\:' | \
	49 cat - /gscratch/srlab/strigg/analyses/20181004/*.deduplication_report.txt > /gscratch/srlab/strigg/analyses/20181004/zr2096_mapping_dedup_summary.txt
	50 #clean up summary report
	51 !sed 's/Mapping\ efficiency\://g' /gscratch/srlab/strigg/analyses/20181004/zr2096_mapping_dedup_summary.txt | \
	52 sed 's/Total\ number\ duplicated\ alignments\ removed\://g' | \
	53 sed 's/ //g' | awk '{print $1}' > /gscratch/srlab/strigg/analyses/20181004/zr2096_mapping_dedup_summary_clean.txt
	55 #sort bams
	56 %%bash
	57 find /gscratch/srlab/strigg/analyses/20181004/*deduplicated.bam| \
	58 xargs basename -s _s1_R1_bismark_bt2_pe.deduplicated.bam | \
	59 xargs -I{} samtools \
	60 sort /gscratch/srlab/strigg/analyses/20181004/{}_s1_R1_bismark_bt2_pe.deduplicated.bam \ 
	61 -o /gscratch/srlab/strigg/analyses/20181004/{}_dedup.sorted.bam