/gannet/Atumefaciens/20190312_cvir_gonad_bismark/total_reads_bismark

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

Examined all read pairs run with Bismark to compare alignment/coverage.

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FILES

- total_reads_summary.txt: Bismark stdout. Contains "final alignment" report at end of file (~ last 30 lines).

- bismark_cytosine_coverage.txt.CpG_report.txt: Full-genome CpG sequencing coverage report; similar to BAM file.

- bismark_summary_report.html: HTML version of "bismark_summary_report.txt" providing graphical view of summary data, but also includes some calculations to determine percentages, instead of just raw counts.

- bismark_summary_report.txt: Raw counts of mapping/methylation statistics.

- C*.txt: Bismark "intermediate" files (methylation conversions)

- cvir_bsseq_all_pe_R1_bismark_bt2_pe.bam: Bismark BAM file.

- cvir_bsseq_all_pe_R1_bismark_bt2_pe.bedGraph.gz: Bismark bedgraph.

- cvir_bsseq_all_pe_R1_bismark_bt2_pe.bismark.cov.gz: Bismark coverage file. Used to generate cytosine coverage file.

- cvir_bsseq_all_pe_R1_bismark_bt2_pe.M-bias.txt: Methylation bias report.

- cvir_bsseq_all_pe_R1_bismark_bt2_PE_report.html: HTML version of Bismark processing (*.report.txt). Useful visualizations of alignment data and methylation contexts.

- cvir_bsseq_all_pe_R1_bismark_bt2_PE_report.txt: Alignment and methylation report. Includes Birmark run parameters and Bismark run time.

- cvir_bsseq_all_pe_R1_bismark_bt2_pe.sorted.bam: Sorted BAM file (samtools).

- cvir_bsseq_all_pe_R1_bismark_bt2_pe.sorted.bam.bai: Indexed BAM file (samtools index).

- cvir_bsseq_all_pe_R1_bismark_bt2_pe_splitting_report.txt: Cytosine methylation report.


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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