PICRUSt工具使用过程中的概念理解

PICRUSt工具使用过程中的概念理解

1. MiSeq 2x250 16S V4 下机测序数据经下面pipeline代码转换为OTU table

#!/bin/bashif [ x$usearch == x ] ; thenecho Must set $usearch >> /dev/stderrexit 1
firm -rf ../out
mkdir -p ../out
cd ../out# Merge paired reads
# Add sample name to read label (-relabel option)
# Pool samples together in raw.fq (Linux cat command)
for Sample in Mock Soil Human Mouse
do$usearch -fastq_mergepairs ../data/${Sample}*_R1.fq -fastqout $d.fq -relabel $Sample.cat $d.fq >> d.fq
done# Strip primers (V4F is 19, V4R is 20)
$usearch -fastx_d.fq -stripleft 19 -stripright 20 -fastqout stripped.fq# Quality filter
$usearch -fastq_filter stripped.fq -fastq_maxee 1.0 -fastaout filtered.fa -relabel Filt# Find unique read sequences and abundances
$usearch -fastx_uniques filtered.fa -sizeout -relabel Uniq -fastaout uniques.fa# Make 97% OTUs and filter chimeras
$usearch -cluster_otus uniques.fa -otus otus.fa -relabel Otu# Denoise: predict biological sequences and filter chimeras
$usearch -unoise3 uniques.fa -zotus zotus.fa##################################################
# Downstream analysis of OTU sequences & OTU table
# Can do this for both OTUs and ZOTUs, here do
# just OTUs to keep it simple.
################################################### Make OTU table
$usearch -d.fq -otus otus.fa -otutabout 

2. OTU table 经过 PICRUSt 工具 转换为 KEGG_ID table(表中的数字代表靶到该OTU或KEGG上的reads数量)