wolfv

name: CI

on:
  push:
    branches:
    - main
  pull_request:
    branches:
    - main

sirselim

Jetson Xavier basecalling notes

initial basecalling runs

'fast' flip-flop calling on the Jetson Xavier

guppy_basecaller --disable_pings --compress_fastq -c dna_r9.4.1_450bps_fast.cfg -i flongle_fast5_pass/ -s flongle_test2 -x 'auto' --recursive 

elowy01

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

jaskiratr

# Source: https://stackoverflow.com/a/43317244
$path = ".\aws-ec2-key.pem"
# Reset to remove explict permissions
icacls.exe $path /reset
# Give current user explicit read-permission
icacls.exe $path /GRANT:R "$($env:USERNAME):(R)"
# Disable inheritance and remove inherited permissions
icacls.exe $path /inheritance:r

perrygeo

FROM python:3.6-slim-stretch

ADD requirements.txt /tmp/requirements.txt

RUN apt-get update && \
    apt-get install -y \
        build-essential \
        make \
        gcc \
        locales \

ipurusho

###Download STAR### Obtain STAR source from https://github.com/alexdobin/STAR

Add the following to your .bashrc file and source it: export PATH=/path/to/STAR/bin/:$PATH

###Generate Reference Genome

crazyhottommy

#!/bin/bash
# function Extract for common file formats

function extract {
 if [ -z "$1" ]; then
    # display usage if no parameters given
    echo "Usage: extract <path/file_name>.<zip|rar|bz2|gz|tar|tbz2|tgz|Z|7z|xz|ex|tar.bz2|tar.gz|tar.xz>"
 else
    if [ -f "$1" ] ; then
        NAME=${1%.*}