sbamin

## add following to the end of ~/.bash_profile assuming ~/.bash_profile takes the precedence over ~/.profile (if present), ~/.bash_profile, or other bash configs.
## for zsh or other shells, you may need to tweak following code.
## Be careful "resetting" PATH variable and know the implications of PATH variable being either empty or missing critical system paths!

################################### SET PATH ###################################
## User specific environment and startup programs
## Rewriting PATH ##
## We want user and anaconda paths to precede system paths, esp. this string:
## /usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin which contains
## most of system default libs,

taoliu

#!/bin/bash
#
# This script will find the consensus peak regions from peak files (in
# BED format) of multiple samples by:
#
# 1. Converting the peak file of each sample into non-overlapping 3
# cols BED file and concatenating them;
#
# 2. Sorting the concatenated file and Building a genome coverage
# track in BedGraph, of which the value (the 3rd col) indicates the

vasantm

# code source for plotting
# https://www.datanovia.com/en/blog/ggplot-title-subtitle-and-caption/
# get source filename SO quest: http://stackoverflow.com/q/1815606/946850
# get source fielname answer: https://stackoverflow.com/a/20282846
# if you do use a hash, you will have to  save these to a csv or write 
# a DB, perhaps an sqlite file that has the entry 
# for the source file and corresponding hash to keep track of the
# hashes or just use filename and proj_dir,
# and display that if you want to keep it simple, 
# open and reproducible

sbamin

--[[
## Modulefile in lua syntax
## Author: Samir Amin

## Read about Lmod
## https://lmod.readthedocs.io/en/latest/015_writing_modules.html
## https://lmod.readthedocs.io/en/latest/050_lua_modulefiles.html
## https://lmod.readthedocs.io/en/latest/020_advanced.html
--]]

michaelmhoffman

(defun new-copyright ()
  "Generate new copyright string."
  (format-time-string "Copyright %Y Michael M. Hoffman <michael.hoffman@utoronto.ca>"))

(define-auto-insert 'python-mode
  `(
    "Description: "
    "#!/usr/bin/env python3.6" \n
    "\"\"\"" (setq basename (buffer-file-basename)) ": " str \n
    "\"\"\"" \n \n

k3yavi

DATASETS = ["PBMC_8K", "PBMC_4k"]

SALMON = "$BINS/salmon-0.14.0_linux_x86_64/bin/salmon"

rule all:
  input: expand("quants/{dataset}/alevin/quants_mat.gz", dataset=DATASETS)

rule salmon_quant:
    input:
        r1 = "reads/{sample}_1.fastq",

mdozmorov

# https://www.biostars.org/p/63225/

FILE=VLI9_AA_S60_L008_R1_001.fastq.gz

zcat $FILE | head -n 40 | awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | awk 'BEGIN{min=100;max=0;}{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END{if(max<=74 && min<59) print "Phred+33"; else if(max>73 && min>=64) print "Phred+64"; else if(min>=59 && min<64 && max>73) print "Solexa+64"; else print "Unknown score encoding";}'

crazyhottommy

Three gotchas when using R for Genomic data analysis

During my daily work with R for genomic data analysis, I encountered several instances that R gives me some (bad) surprises.

1. The devil 1 and 0 coordinate system

read detail here https://github.com/crazyhottommy/DNA-seq-analysis#tips-and-lessons-learned-during-my-dna-seq-data-analysis-journey

some files such as bed file is 0 based. Two genomic regions: