Tuesday, August 19, 2014

#installing Fasta_reader (needed to run script for stats on Trinity assembly)
#first need to install npm
brew install node
vi server.js
#paste the following
var http = require('http'); http.createServer(function (req, res) { res.writeHead(200, {'Content-Type': 'text/plain'}); res.end('Hello World\n'); }).listen(8124, "127.0.0.1"); console.log('Server running at http://127.0.0.1:8124/');
#ESC wq!

#to check if it works
node server.js

npm install fastareader

WOOPS! nevermind! All of this stuff is already installed with Trinity. To run TrinityStats.pl, it cannot be run alone. You must navigate to the directory in which it is found.
###################
#   Ar_jam MOE    #
###################
#combine data from Lanes 1 & 2
cat Arjam_MOE* >> DR_004_Arjam_MOE_assembled.fasta
sudo perl /Volumes/Spare/transcriptomes/Trinity/util/TrinityStats.pl /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/DR_004_Arjam_MOE_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 140189
Total trinity components: 63956
Percent GC: 55.16

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 4088
Contig N20: 3085
Contig N30: 2434
Contig N40: 1927
Contig N50: 1502

Median contig length: 426
Average contig: 826.50
Total assembled bases: 115865619


#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 3860
Contig N20: 2862
Contig N30: 2212
Contig N40: 1726
Contig N50: 1310

Median contig length: 440
Average contig: 793.55
Total assembled bases: 50752060 
###################
#   Ar_jam VNO    #
###################
#combine data from Lanes 1 & 2
cat Arjam_VNO* >> DR_011_Arjam_VNO_assembled.fasta
sudo perl /Volumes/Spare/transcriptomes/Trinity/util/TrinityStats.pl /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/DR_011_Arjam_VNO_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 138142
Total trinity components: 61477
Percent GC: 55.51

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 4735
Contig N20: 3550
Contig N30: 2822
Contig N40: 2240
Contig N50: 1741

Median contig length: 455
Average contig: 920.11
Total assembled bases: 127106357


#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 3855
Contig N20: 2871
Contig N30: 2270
Contig N40: 1814
Contig N50: 1436

Median contig length: 467
Average contig: 848.36

Total assembled bases: 52154403
###################
#   Mo_red MOE    #
###################
#combine data from Lanes 1 & 2
cat Mored_MOE* >> DR_013_Mored_MOE_assembled.fasta
sudo perl /Volumes/Spare/transcriptomes/Trinity/util/TrinityStats.pl /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/DR_013_Mored_MOE_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 245573
Total trinity components: 100799
Percent GC: 56.14

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 5311
Contig N20: 4036
Contig N30: 3304
Contig N40: 2703
Contig N50: 2118

Median contig length: 406
Average contig: 960.45
Total assembled bases: 235861464


#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 4140
Contig N20: 2880
Contig N30: 2105
Contig N40: 1512
Contig N50: 1053

Median contig length: 377
Average contig: 685.78

Total assembled bases: 69126334

###################
#   Mo_red VNO    #
###################
#combine data from Lanes 1 & 2
cat Mored_VNO* >> DR_013_Mored_VNO_assembled.fasta
sudo perl $TRINITY_HOME/util/TrinityStats.pl DR_013_Mored_VNO_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 163233
Total trinity components: 70319
Percent GC: 55.74

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 4648
Contig N20: 3450
Contig N30: 2778
Contig N40: 2186
Contig N50: 1709

Median contig length: 430
Average contig: 883.37
Total assembled bases: 144195048


#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 3865
Contig N20: 2811
Contig N30: 2110
Contig N40: 1605
Contig N50: 1187

Median contig length: 427
Average contig: 754.88

Total assembled bases: 53082440


###################
#   Mo_bla MOE    #
###################
cat Mobl_MOE* >> DR_091_Mobl_MOE_assembled.fasta
sudo perl $TRINITY_HOME/util/TrinityStats.pl DR_091_Mobl_MOE_assembled.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity transcripts: 249551
Total trinity components: 115871
Percent GC: 54.01

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 4786
Contig N20: 3549
Contig N30: 2741
Contig N40: 2123
Contig N50: 1598

Median contig length: 335
Average contig: 763.67
Total assembled bases: 190573978


#####################################################
## Stats based on ONLY LONGEST ISOFORM per COMPONENT:
#####################################################

Contig N10: 3761
Contig N20: 2670
Contig N30: 1971
Contig N40: 1426
Contig N50: 989

Median contig length: 344
Average contig: 636.73

Total assembled bases: 73778325

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