James Ferguson Psy-Fer
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Psy-Fer
/ fastq_line_by_line.r
Created
September 6, 2018 17:03
Quick example of reading a fastq file line by line in R
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| con <- file("test.fastq", "r") | |
| c <- 0 | |
| while ( TRUE ) { | |
| line = readLines(con, n = 1) | |
| if( length(line) == 0 ) { | |
| break | |
| } | |
| c <- c + 1 | |
| if(c == 1){ | |
| print(line) |
Psy-Fer
/ reorgcirc.py
Last active
May 3, 2021 09:20
re-organise circular assembly using given search sequence
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| import os | |
| import sys | |
| import argparse | |
| import edlib | |
| ''' | |
| James M. Ferguson (j.ferguson@garvan.org.au) | |
| Genomic Technologies | |
| Garvan Institute | |
| Copyright 2021 |
Psy-Fer
/ varscan_cmd.sh
Created
May 24, 2021 00:43
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| # where $1 is the sample name. eg sample-0112, for naming scheme sample-0112_merged.bam, etc. | |
| samtools mpileup \ | |
| -f nCoV-2019.reference.fasta \ | |
| --max-depth 1000 \ | |
| --positions nCoV-2019.reportable_region.bed \ | |
| ${1}_merged.bam -o ${1}_merged.mpileup | |
| java -jar VarScan.v2.4.3.jar mpileup2snp \ |