WORKSHOPS

DATA WRANGLERS ANONYMOUS

... a series that provides a semi-regular "study group" where people come together with their computers to work on whatever problems they have / learn about whatever topics they want to know more about.

  • Upcoming: 5/19

  • April 21, 2015 - converting UCSC IDs to Gene Names using Table Browser and BioMart

  • March 17, 2015 - identifying enriched gene sets using piano

  • February 17, 2015 - estimating how many sequencing reads are needed using preseq

  • January 20, 2015 - update on Gall Lab RNA-seq analysis pipeline

  • December 16, 2014 - towards reproducible research with csvkit and jq

  • PH525x - 7/22 7/29 8/5 8/26 9/9 10/7 10/14 10/21 10/28 11/4 11/18/14

  • July 15, 2014 - extracting polyA junction reads using awk and softclipping (sample unmap and remap)

  • June 17, 2014 - wrangling bwa and blat output into FileMaker using sed and awk (sample data)

  • June 3, 2014 - sed basics: substitute action, line patterns, regular expressions

  • May 20, 2014 - displaying genome-wide data with Circos (sample data and plot)

  • April 15, 2014 - publication quality gene coverage plots with trackViewer (sample1 sample2)

  • March 18, 2014 - HTSeq and BEDTools coverage, intersect, gtf2bed (sample data)

  • February 18, 2014 - DESeq: loading HTSeq counts, sample QC, inference testing (sample data)

  • January 28, 2014 - .SAM files: format specifications, optional flags, SAM flags, SAMtools, CIGAR string

  • January 7, 2014 - Bash scripting: nano editor, variables, for loops, command line arguments

  • December 19, 2013 - R basics: loading data from a file, subsetting matrices, calculating summary statistics, simple plotting

PERL THURSDAYS

NITTY GRITTY WORKFLOWS

... a "nuts and bolts" series that provides a forum to discuss the ins and outs of deep sequencing analysis pipelines. This is primarily a technical series where speakers describe not only what programs they used, but why they chose the specific parameters they did. Most fun happens when something is not working and we get to brainstorm on possible solutions. This interaction helps troubleshoot and establish "best practices".

  • Upcoming: 

  • May 5, 2015 - Zhao Zhang - identifying transposon insertions in mixed populations with TEMP

  • April 7, 2015 - Pavol Genzor - re-producing analysis of HITS-CLIP data

  • March 3, 2015 - Valeriya Gaysinskaya - analyzing DNA methylation with Bismark/bsseq

  • February 3, 2015 - Bill Kupiec - bringing R code alive on the web with Shiny

  • December 2, 2014 - Brendan Miller - quantitating repetitive elements using Kraken

  • May 6, 2014 - James Justice - a new pipeline to identify retroviral integration sites

  • April 1, 2014 - Zehra Nizami - measuring pre-mRNA using bedtools

  • March 4, 2014 - Sophia Ottleben - searching for transposon somatic mosaicism with awk

  • February 4, 2014 - Shekerah Primus - identify alternative splicing using DEXSeq

  • December 3, 2013 - Allan Spradling - studying genome rearrangements using paired-end reads

  • November 5, 2013 - Pavol Genzor - peak analysis using MACS and MEME

  • October 1, 2013 - Anna McGeachy - two-factor analysis using GLMs and DESeq

  • September 10, 2013 - Safia Malki - separating miRNAs from siRNAs from piRNAs, Galaxy

  • August 6, 2013 - Rosa Alcazar - identifying miRNAs with miRDeep2

  • June 25, 2013 - Erin Jimenez - mRNA-Seq quality control, cuffdiff2 vs deseq

  • June 4, 2013 - Will Yarosh - searching for DNA structural variants using igvtools and awk

  • March 12, 2013 - Gaëlle Talhouarne - motif finding, detecting circles

  • January 29, 2013 - Mike Harris - heterogeneous samples, calculating enrichment

  • January 4, 2013 - Eric Mills - count tables, variance estimation with DESeq

  • December 18, 2012 - Ethan Greenblatt - mapping errors, unmapped reads

  • November 27, 2012 - Lydia Li - quality control using CummeRbund, UCSC kgXref table

  • November 6, 2012 - Frederick Tan - transcriptome assembly, GO analysis with blast2go