charles-plessy

cutadapt -g ^GACTCATCCCATTTTTGAGTCCGATTTCGATTGTCTAACAG -o ${SAMPLE}_SL_R1.fq -p ${SAMPLE}_SL_R2.fq --untrimmed-output ${SAMPLE}_noSL_R1.fq --untrimmed-paired-output ${SAMPLE}_noSL_R2.fq ${SAMPLE}_BC_ATCATA_READ1.fq ${SAMPLE}_BC_ATCATA_READ2.fq

charles-plessy

plate <- data.frame( Row = rep(LETTERS[1:16], 24)
                   , Col = unlist(lapply(1:24, rep, 16)))

plate$Row <- factor(plate$Row, levels=rev(levels(plate$Row)))

set.seed(1)
plate[001:096, "val"] <- rpois(96,10)
plate[097:384, "val"] <- rpois(96, 6)

# Plot with ggplot2

charles-plessy

NOTE: this patch is not needed anymore, since NIST started to distribute
the spike sequences at the following URL.

https://www-s.nist.gov/srmors/certificates/documents/SRM2374_putative_T7_products_NoPolyA_v1.fasta

Description: Adds linker sequences to ERCC (NIST SRM2374) spikes
 The U.S. National Institute of Standards and Technology (NIST)
 provides the sequence of the inserts that have been cloned
 into plasmids to create the External RNA Controls Consortium
 (ERCC) spikes.  These spikes are commercially available as

charles-plessy

# Charles Plessy, RIKEN
# https://creativecommons.org/publicdomain/zero/1.0/

# curl --silent https://gist.githubusercontent.com/charles-plessy/9dbc8bc98fb773bf71b6/raw | tee getAndParseGencode.bash | bash

# Comments starting with ##!! signal Linux/OSX portability traps

# Setup
# =====