Josh Herr jrherr

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I am an Assistant Professor at the University of Nebraska. I study the genomics and metagenomics of plant-microbe interactions with a focus on mycology.

148 followers · 135 following

University of Nebraska
Lincoln, NE, USA
http://joshuaherr.com

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jrherr / excel_my_barplot.R

Created January 13, 2016 16:07 — forked from mw55309/excel_my_barplot.R

R code to create Excel-like barplot

	x <- data.frame(d=runif(12), g=rep(1:4, each =3))

	my.col <- c("deepskyblue3","darkorange2","darkgray","gold")

	spacer <- c(1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1)

	bw <- 0.8

	xmax <- (sum(spacer) * bw) + (nrow(x) * bw)

jrherr / read_hdf5_biom.R

Created December 8, 2015 17:55 — forked from jnpaulson/read_hdf5_biom.R

Hacks to load an hdf5 biom file and be able to add it to metagenomeSeq or phyloseq

	source("http://bioconductor.org/biocLite.R")
	biocLite(c("rhdf5","biom"))
	library(rhdf5)
	library(biom)

	# This generates the matrix columns-wise
	generate_matrix <- function(x){
	indptr = x$sample$matrix$indptr+1
	indices = x$sample$matrix$indices+1
	data = x$sample$matrix$data

jrherr / fq-strip-contam.sh

Last active September 9, 2015 15:28 — forked from standage/fq-strip-contam.sh

Procedure for removing contaminants from paired-end sequence data. The bwa-mem algorithm is used to map reads against a database of contaminants, a small Perl one-liner is used to filter out reads that map to the contaminants, the SAM data is converted to BAM format, which is then fed (via process substitution) to Tophat's bam2fastx to convert b…

	# -q: output in Fastq format
	# -Q: ignore BAM quality flags
	# -P: paired-end data
	bam2fastx -qQP -o clean.fq <(bwa mem contaminants.fasta reads.1.fq reads.2.fq \| \
	perl -ne '@v = split(/\t/); print if(m/^@/ or ($v[1] & 4 and $v[1] & 8))' \| \
	samtools view -bhS -)

jrherr / genome_plots.r

Last active August 29, 2015 14:27 — forked from roblanf/genome_plots.r

Make plots about genome sequencing, size, and gene content

	source("http://bioconductor.org/biocLite.R")
	biocLite("genomes")

	library(genomes)
	library(ggplot2)

	valid <- c("released", "created", "submitted")

	data(proks)
	update(proks)

jrherr / search_download.md

Last active August 29, 2015 14:26 — forked from sckott/search_download.md

occ_search and occ_download

to get similar results for GBIF search and download APIs

Load rgbif

library("rgbif")

occ_search() method

jrherr / 01.cmake

Last active August 29, 2015 14:22 — forked from anonymous/01.cmake

	Wed Jun 10 19:52:40 +0000 2015

	cmake
	..
	-DCMAKE_C_FLAGS_RELEASE=
	-DCMAKE_CXX_FLAGS_RELEASE=
	-DCMAKE_INSTALL_PREFIX=/home/ubuntu/.linuxbrew/Cellar/spades/3.5.0
	-DCMAKE_BUILD_TYPE=Release
	-DCMAKE_FIND_FRAMEWORK=LAST
	-DCMAKE_VERBOSE_MAKEFILE=ON

jrherr / remove_redundant_sequences

Created May 18, 2015 17:47

remove redundant sequences from fasta file

sed -e '/^>/s/$/@/' -e 's/^>/#/' name.fasta | tr -d '\n' | tr "#" "\n" | tr "@" "\t" | sort -u -t '  ' -f -k 2,2  | sed -e 's/^/>/' -e 's/\t/\n/'

jrherr / gist:1ae494fc5396a8b49cd4

Created May 14, 2015 19:33

sub scripts

	# kill all qsub jobs
	qselect -u $USER -S -Q \| xargs qdel

jrherr / bamfilter_oneliners.md

Last active September 9, 2015 15:19 — forked from davfre/bamfilter_oneliners.md

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please comment or extend with additional/faster/better solutions.

BWA mapping (using piping for minimal disk I/O)

jrherr / gist:2c5fed226a1a63f5643a

Created February 8, 2015 16:55

Rename SPAdes output fasta headers line for pipeline

sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.name}\1 \2/g" $input > $output

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