forked from CorrieRB/16S_ITS_Analysis
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathSequence_Analysis.R
39 lines (27 loc) · 1.83 KB
/
Sequence_Analysis.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
#############################################################################################
#----------------------16S_ITS Analysis-Blasting Sequences-----------------------------------
#############################################################################################
######Place cursor on line to be run or highlight and press run on top right hand corner#####
##Notes:
##Name files with the following convention
###----YYYY_MM_DD_16S_Accession#_FWD
###----YYYY_MM_DD_ITS_Accession#_REV
#Quality summary will be put in Results Folder
#fasta contigs will be put in Fasta_Sequences Folder
#1.----------------Install packages and sourcing functions--------------------------------------
source("Analyze_Sanger_Functions.R")
source("Blast_Analysis_functions.R")
#2.------------------Trim, merge and generating consensus sequences-----------------------------
#for generating contig from forward and reverse reads in a sequencing file
#change path to location of raw sequencing data
analyze.sequences(path ="../Raw_data/Plate_2021_02_24_16S")
#for trimming and generating fasta sequence for a single read forward or reverse
#change readFileName to sequence of interest including sequence location
analyze.single.sequence(readFileName = "../Raw_data/Plate_2021_02_24_16S/2021_02_24_16S_STAU25923_FWD.ab1", readFeature = "Reverse Read")
#3.---------------------------------Blast-----------------------------------------------------
#for search against 16S and ITS databases
#change Blastpath to location of fasta sequences
Blast.Files(Blastpath = "../Fasta_Sequences", DBname = "_rRNA")
#for search against nucleotide database
#change Blastpath to location of fasta sequences
Blast.Files(Blastpath = "../Fasta_Sequences_nucleotide_search", blast16Sdb = "../ncbi-blast-2.13.0+/db/nt", blastITSdb = "../ncbi-blast-2.13.0+/db/nt", DBname = "_nucleotide")