sirselim

IlmnID	Infinium_Design_Type	Genome_Build	CHR	MAPINFO	Probe_SNPs	Probe_SNPs_10	UCSC_RefGene_Name	ks.score	ks.pval	logP	median_MS	median_HC	median_diff	abs_median_diff	adjP	UCSC_RefGene_Group
cg19159092	II	37	1	856059	rs28534711		FLJ39609	0.54	0.001401357	2.853451255	0.369697583	0.235456657	0.134	0.134	1	TSS1500
cg01394461	II	37	1	887576			NOC2L	0.58	0.000405656	3.391842167	0.605999215	0.765577211	-0.16	0.16	1	Body
cg24004483	I	37	1	944783				0.42	0.029913567	1.524131795	0.421027063	0.567238531	-0.146	0.146	1	
cg22627753	II	37	1	988623			AGRN	0.5	0.00432085	2.364430777	0.791366927	0.61083939	0.181	0.181	1	Body
cg09864227	I	37	1	1008207				0.58	0.000405656	3.391842167	0.826697106	0.724967037	0.102	0.102	1	
cg00300303	II	37	1	1067223				0.5	0.00432085	2.364430777	0.623355286	0.774244123	-0.151	0.151	1	
cg15822328	II	37	1	1072197				0.5	0.00432085	2.364430777	0.431884651	0.270809266	0.161	0.161	1	
cg08474826	II	37	1	1099630				0.42	0.029913567	1.524131795	0.587936074	0.446153689	0.142	0.142	1	
cg06967105	II	37	1	1

sirselim

#!/bin/bash
## small bash script to download and reformat dbNSFP for pipeline 
## Miles Benton
## created: 2018-01-13
## modified: 2019-08-21

# Set to dbNSFP version to download and build
version="4.0a"
#TODO: add an option to 'scrape' this from the url to always return latest version
# define thread number for parallel processing where able

sirselim

import streamlit as st
import pandas as pd
import numpy as np

st.title('Uber pickups in NYC')

DATE_COLUMN = 'date/time'
DATA_URL = ('https://s3-us-west-2.amazonaws.com/'
            'streamlit-demo-data/uber-raw-data-sep14.csv.gz')

sirselim

# handy scripts for bioinformatics
# A collection of scripts that I find useful.

## convert bam to cram format

# define reference genome (required for cram format)
# GENOME="/data/publicData/genomes/human/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna" # hg38
GENOME="/data/publicData/genomes/human/GRCh37/hs37d5.fa" # hg19
# find all bam files in current dir and convert to cram
find . -name "*.bam" | sed "s/\.bam$//" | xargs -I {} -P 36 samtools view -@ 4 -T $GENOME -C -o {}.cram {}.bam

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 

sirselim

Nanopore basecalling on Google Colab

---

NOTE: this whole idea is the brain child of Jürgen Hench. He got it up and running and posted about it here. I am merely wrapping the idea in a hopefully easy to follow set of instructions for people to test themseleves.

---

This notebook describes processing of Nanopore sequencing data (fast5 files) in a Google Colab interactive notebook environment. This is made possible by utalising the GPU enabled runtime that is available via Colab.

sirselim

#!/bin/bash
# author: Miles Benton
# created: 31st Aug 2021
# modified: 31st Aug 2021
#
# Notes:
# small bash script that automates installing and setting up ONT minknow and GPU
# guppy for live basecalling and GPU processing of nanopore data on Ubuntu 21.04 
# based releases.
#