seb-mueller

# source of this function: https://github.com/hms-dbmi/UpSetR/issues/85#issuecomment-327900647
fromList <- function (input) {
  # Same as original fromList()...
  elements <- unique(unlist(input))
  data <- unlist(lapply(input, function(x) {
      x <- as.vector(match(elements, x))
      }))
  data[is.na(data)] <- as.integer(0)
  data[data != 0] <- as.integer(1)
  data <- data.frame(matrix(data, ncol = length(input), byrow = F))

seb-mueller

export BLASTDB=/data/public_data/NCBI/NCBI_all/ #and specify the db as -db nt |or -db /data/public_data/NCBI/NCBI_nt/nt
export PATH=/applications/UCSC-tools/:/applications/ncbi-blast+/ncbi-blast-2.2.30+/bin/:$PATH

#subsetting and converting into fasta
file=sample.fq.gz
filefa=${file%.fq.gz}_subset.fa
n=400000
zcat $file | head -n $n > ${file%.fq.gz}_subset.fq
fastqToFa ${file%.fq.gz}_subset.fq $filefa