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Collection of scripts written for the Belmonte lab.

siRNA Project (Summer 2019):

  • analysis_of_siRNA_meth_intersect.R: Compute the average methylation ratio per siRNA locus from Shortstack output based on the output of intersectBed using the bed files of both data sets prepared in this project.
  • Do a local blastn of a given query file and print the top hit for each query sequence. Essentially a python wrapper and parser. Saves the full blast results in a .xml file as a byproduct.
  • build_cytosine_bed4_siRNA_version.R: Edited version of the same script in the Methylation Project. Has a lower filtering threshold and updated input file locations.
  • intersectBed_cmds.txt: Documentation of commands used to intersect the methylation and ShortStack siRNA bed files.
  • Create bed4 files for intersection from the .xml blastn outoput file of ShortStack siRNAs.
  • shortstack_cmds.txt: Documentation of commands used for ShortStack analysis.
  • standalone_blastn_adventures.txt: Documentation of commands used for setting up and running blastn locally.

Methylation Project (Summer 2017):

  • 2017_08_01_bsmap_methylKit.R: Analyse data from BSMAP methylation call files with methylKit (Also create BED4 DMR files)
  • bedtools_cmds.txt: Bash commands to create gene flanks and intersect gene/flanks with DMRs (Differentially Methylated Regions)
  • build_cytosine_bed4.R: Make BED4 files from our BSMAP methylation call files (after they went throught
  • build_gene_expression_bed5.R: Make BED5 files of differential gene expression data. The information is taken from several files and put together in a useful format.
  • correlate_meth_gene_expr.R: Older of the 2 correlation scripts, methylation level in a DMR vs gene expr the DMR overlaps with or flanks. Not very pretty or useful results-wise because it used older fpkm data and slightly messier input but could be useful as a reference.
  • corr_mean_meth_vs_expr.R: Correlates the mean methylation ratio in a feature (gene or its flanks) with that feature's expression level (fpkms from cuffdiff). Makes scatterplots.
  • extract_filter_intersectBed.R: Process the output of bedtools_cmds into a more usable format. Includes cmds for SeqEnrich prep
  • methylation_heatmap_and_bargraph.R: Visualize methylation data by context, sample, and chromosome, visualize transposable element, gene, and CpG island density. (Mostly bar charts currently, heatmaps are not turning out great)

Pipeline (Summer 2016):

  • SeqAnalysisPipeline: (perl) Guides user through the Belmonte lab's Sequencing Analysis Pipeline (Trimmomatic, TopHat2 with Bowtie2-build, Cuffquant, Cuffnorm, and CuffDiff) using cmd line prompts. Does preliminary error checking, saves a copy of the commands that were run, and organizes the output. Intructions/tutorial PDF file included in repository.

Formatting Programs (Summer 2016):

  • ExtractLines: Extract lines that contain a target string (old script, grep is much more efficient)
  • PWM_to_IUPAC: Convert PWM (Position Weight Matrix) to IUPAc sequences (java)
  • ProcessedGOFormatter: Process SeqEnrich GO term output into a more usable format, filters p-values (old script, could do much better in R)


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