khemlalnirmalkar

metaphlanToPhyloseq <- function(
  metaphlandir,
  metadat=NULL,
  simplify=TRUE){
  ## tax is a matrix or data.frame with the table of taxonomic abundances, rows are taxa, columns are samples
  ## metadat is an optional data.frame of specimen metadata, rows are samples, columns are variables
  ## if simplify=TRUE, use only the most detailed level of taxa names in the final object
  ## metaphlanToPhyloseq("~/Downloads/metaphlan_bugs_list")
  .getMetaphlanTree <- function(removeGCF=TRUE, simplify=TRUE){
    if (!requireNamespace("ape")) {

khemlalnirmalkar

>Illumina Single End Apapter 1					
ACACTCTTTCCCTACACGACGCTGTTCCATCT
>Illumina Single End Apapter 2					
CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
>Illumina Single End PCR Primer 1				
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Illumina Single End PCR Primer 2				
CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
>Illumina Single End Sequencing Primer			
ACACTCTTTCCCTACACGACGCTCTTCCGATCT

khemlalnirmalkar

#!/bin/bash
usage ()
{
    echo ""
    echo "Usage : `basename $0` <tableL6.txt> <L6_clean.tsv>"
    echo ""
    exit
}

if [ "$1" = "" ]; then