protocols and programs

   
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Lab Scripts:
https://github.com/nagreme/belmonte_lab

Formatting Programs:
  • 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)
Methylation Project:
  • 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)
  • 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:
  • 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.
  •  https://github.com/nagreme/SeqEnrich


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  • Home
  • The Belmonte Lab
  • Photos and Fun Stuff
  • Microscopy
  • Research Projects
  • Publications
  • News and Media
  • Collaborators
  • Teaching
  • Protocols and Scripts