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/bash

if [ x$usearch == x ] ; then
	echo Must set \$usearch >> /dev/stderr
	exit 1
fi

rm -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 $Sample.merged.fq -relabel $Sample.
	cat $Sample.merged.fq >> all.merged.fq
done

# Strip primers (V4F is 19, V4R is 20)
$usearch -fastx_truncate all.merged.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 -otutab all.merged.fq -otus otus.fa -otutabout otutab_raw.txt

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)

OTU_ID	Sample1	Sample2	Sample3	Sample4
1	100	80	60	90
2	50	60	70	50
3	40	60	60	40
4	90	80	50	80

 

KEGG_ID	Sample1	Sample2	Sample3	Sample4
ko1234	90	80	40	40
ko2556	60	60	50	10
ko6948	60	18	26	34
ko6549	66	93	10	80