/gannet/Atumefaciens/20190312_cvir_gonad_bismark

Exploration of C.virginica CpG coverage from MBD BS-seq project.

Examined varying number of subsets of read pairs to run with Bismark to compare alignment/coverage.

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FILES

- 20190312_cvir_gonad_bismark.sh: SBATCH script to run job on Mox.

- avg_reads_bismark: Directory for Bismark using the average number of read pair subset.

- cvir_bsseq_all_pe_R1.fastq.gz: Concatenated R1 FastQ gzip file.

- cvir_bsseq_all_pe_R2.fastq.gz: Concatenated R2 FastQ gzip file.

- cvir_bsseq_pe_all_R1.list: List of R1 input FastQ used for concatenation.

- cvir_bsseq_pe_all_R2.list: List of R2 input FastQ used for concatenation.

- half_avg_reads_bismark: Directory for Bismark using 50% the average number of read pair subset.

- half_total_reads_bismark: Directory for Bismark using 50% the total number of read pair subset.

- library_counts.txt: Number of reads in each input FastQ used for concatenation.

- slurm-687218.out: SLURM output file from first run (stderr/stdout).

- slurm-734830.out: SLURM output file from second run (stderr/stdout).

- system_path.log: Values stored in Sam's system $PATH on Mox.

- total_reads_bismark: Directory for Bismark using the total number of read pair subset.

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Notebook:

https://robertslab.github.io/sams-notebook/2019/03/13/Methylation-Analysis-C.virginica-Gonad-MBD-with-Varying-Read-Subsets-with-Bismark-on-Mox.html