Heng Li lh3

NA12878 DirectRNA reads were obtained [here][raw-data] (passed reads only) and aligned with [minimap2][minimap2] v2.5 against the no_alt_analysis_set of GRCh38 plus SIRV contigs. It took <1 wall-clock hour across 16 CPU cores with command-line options: -cx splice -k14 --cs -uf -N20 -t16. Alignments were converted to BED with the misc/splice2bed.js script from minimap2 and then converted to BigBed. Ribosome-related genes (RPL*, RPS*, EEF* and RPSA) were excluded to reduce the file size. The final BigBed is hosted [at OSF][osf-prj].

A UCSC custom track is configured with

track type=bigBed name=NA12878-DirectRNA.minimap2-2.5 useScore=1 visibility=4 itemRgb="On" bigDataUrl=https://files.osf.io/v1/resources/b5nm2/providers/osfstorage/5a2347599ad5a10272ed5739?action=download&version=1&direct

You can access this track with the [following link][direct-link]. A GMAP alignment track is temporarily available [here][gmap]. This track contains 1/4 of reads. GMAP is still running. It will take 4–5 wall-clock

	# download portable samtools binary v1.14 (not the latest version)
	curl -L 'https://zenodo.org/records/5731013/files/htstools-1.14_x64-linux.tar.bz2?download=1' \| tar -jxf - htstools-1.14_x64-linux/samtools
	htstools-1.14_x64-linux/samtools # test run; the following command lines assume "samtools" is on $PATH

	# download minimap2 binary; also easy to compile from the source code
	curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 \| tar -jxf - minimap2-2.28_x64-linux/minimap2

	# download T2T-CHM13v2 analysis set
	curl -L https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0_maskedY_rCRS.fa.gz \| zcat > chm13v2.fa
	samtools faidx chm13v2.fa


	// MIT License
	//
	// Copyright (c) 2018 degski
	//
	// Permission is hereby granted, free of charge, to any person obtaining a copy
	// of this software and associated documentation files (the "Software"), to deal
	// in the Software without restriction, including without limitation the rights
	// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
	// copies of the Software, and to permit persons to whom the Software is

	#creates a base image from condo
	FROM continuumio/miniconda3
	SHELL ["/bin/bash", "-c"]

	COPY environment.yml .

	#run environment
	#RUN conda env create -f environment.yml

	RUN conda init bash

	// To compile:
	// gcc -g -O2 example.c libminimap2.a -lz

	#include <stdlib.h>
	#include <assert.h>
	#include <stdio.h>
	#include <zlib.h>
	#include "minimap.h"
	#include "kseq.h"
	KSEQ_INIT(gzFile, gzread)

	// a combination of inverse square root (see wiki) and inversion: https://bits.stephan-brumme.com/inverse.html
	static inline float mg_sqrtf(float x)
	{
	union { float f; uint32_t i; } z = { x };
	z.i = 0x5f3759df - (z.i >> 1);
	z.f = (1.5f - (x 0.5f * z.f * z.f));
	z.i = 0x7EEEEEEE - z.i;
	return z.f;
	}

	gg:ksw2_ggd.c cli.c ksw2.h
	$(CC) -Wall -g -O2 -o $@ ksw2_ggd.c cli.c

	clean:
	rm -fr .o .dSYM gg

	CREATE TABLE seq (
	checksum TEXT,
	ac TEXT, -- INSDC sequence accession, when available
	len INTEGER, -- could be of type "TEXT"; no need to implement "less than"
	seq TEXT,
	PRIMARY KEY (checksum) -- what about collisions?
	);
	CREATE INDEX seq_len ON seq (len)
	CREATE INDEX seq_ac ON seq (ac) -- different checksums may have the same AC

	#include <stdio.h>

	#define SIMD_SSE 0x1
	#define SIMD_SSE2 0x2
	#define SIMD_SSE3 0x4
	#define SIMD_SSSE3 0x8
	#define SIMD_SSE4_1 0x10
	#define SIMD_SSE4_2 0x20
	#define SIMD_AVX 0x40
	#define SIMD_AVX2 0x80