links

http://cas-genome.cas.unt.edu/dev/cchiu/gsv/homepage.php

http://www.blogger.com/post-create.g?blogID=389511881549409220

http://kashirevanna.blogspot.com/

http://microbiota.org/cgi-bin/ocular/index.cgi

http://www.iulungmicrobiome.org/cgi-bin/login.cgi

TESTING RDP-MULTICLASSIFER

First,
wget http://rdp.cme.msu.edu/download/rdp_multiclassifier.zip
Second,
unzip http://rdp.cme.msu.edu/download/rdp_multiclassifier.zip
cd rdp_multiclassifier

Third, get the input file,
grab a fasta to test, I grab ocular file.

Fourth,
Run the script
/scratch/cc0430/packages/jre1.6.0_20/bin/java -Xmx1g -jar /scratch/cc0430/rdp_multiclassifier/dist/multiclassifier.jar /scratch/cc0430/metagenome/Ocular/454/Fasta/V0021801ss_R1_trimmed.fasta > /scratch/cc0430/scripts/foooooo

the content of foooooo

taxid lineage name rank V0021801ss_R1_trimmed.fasta
0 null Root no rank 21920
1 Root;norank;Bacteria;domain; Bacteria domain 21916
61 Root;norank;Bacteria;domain;"Firmicutes";phylum; "Firmicutes" phylum 10225
62 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class; "Bacilli" class 10220
63 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order; Bacillales order 10216
140 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family; "Staphylococcaceae" family 10212
146 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family;Staphylococcus;genus; Staphylococcus genus 10210
-141 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family;unclassified_"Staphylococcaceae";; unclassified_"Staphylococcaceae" 2
-64 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;unclassified_Bacillales;; unclassified_Bacillales 4
160 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order; "Lactobacillales" order 3
203 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order;Streptococcaceae;family; Streptococcaceae family 3
206 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order;Streptococcaceae;family;Streptococcus;genus; Streptococcus genus 3
more....

Option

--conf= specifies the assignment confidence cutoff used to determine the assignment count in the hierarchical format. Range [0-1], Default is 0.8.

/scratch/cc0430/packages/jre1.6.0_20/bin/java -Xmx1g -jar /scratch/cc0430/rdp_multiclassifier/dist/multiclassifier.jar --conf=0.9 /scratch/cc0430/metagenome/Ocular/454/Fasta/V0021801ss_R1_trimmed.fasta > /scratch/cc0430/scripts/foooooo1

the content of foooooo1

taxid lineage name rank V0021801ss_R1_trimmed.fasta
0 null Root no rank 21920
1 Root;norank;Bacteria;domain; Bacteria domain 21915
61 Root;norank;Bacteria;domain;"Firmicutes";phylum; "Firmicutes" phylum 10221
62 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class; "Bacilli" class 10218
63 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order; Bacillales order 10211
140 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family; "Staphylococcaceae" family 10202
146 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family;Staphylococcus;genus; Staphylococcus genus 10196
-141 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family;unclassified_"Staphylococcaceae";; unclassified_"Staphylococcaceae" 6
-64 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;unclassified_Bacillales;; unclassified_Bacillales 9
160 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order; "Lactobacillales" order 3
203 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order;Streptococcaceae;family; Streptococcaceae family 3
206 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order;Streptococcaceae;family;Streptococcus;genus; Streptococcus genus 3
-63 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;unclassified_"Bacilli";; unclassified_"Bacilli" 4
653 Root;norank;Bacteria;domain;"Actinobacteria";phylum; "Actinobacteria" phylum 10452
654 Root;norank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class; Actinobacteria class 10452
666 Root;norank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Actinobacteridae;subclass; Actinobacteridae subclass 10452
667 Root;norank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Actinobacteridae;subclass;Actinomycetales;order; Actinomycetales order 10452
684 Root;norank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Actinobacteridae;subclass;Actinomycetales;order;Corynebacterineae;suborder; Corynebacterineae suborder 9700
more......


When we use --conf=0.9 the fifth value in every row is getting smaller.

Run RDP SeqMatch

First part:

• Take the first attached file and upload it to http://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp
  
• Select "1" from "KNN matches"
• Click "Submit" (do not close your browser)
• After the job is finished, click the button "download as text file" at the result page.
• Rename the saved file as File1.SeqMatch.KNN
• repeat the above step 2 - 6 for the second attached file and rename the output as File2.SeqMatch.KNN
• repeat the above step 2 - 6 for the third attached file and rename the output as File3.SeqMatch.KNN

Second part:

• Take the first attached file and upload it to http://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp
  
• Select "1" from "KNN matches" and Select "Isolates" from "Source"
• Click "Submit" (do not close your browser)
• After the job is finished, click the button "download as text file" at the result page.
• Rename the saved file as File1.SeqMatch.Source
• repeat the above step 2 - 6 for the second attached file and rename the output as File2.SeqMatch.Source
• repeat the above step 2 - 6 for the third attached file and rename the output as File3.SeqMatch.Source

Setting up BLAST

1. change the path for blast_setup.cgi, blast_run.cgi, blast_result.cgi
2. delete use MyModule::use Store();
3. change the right folder's name on 78 lines on blast_setup.cgi
4. getting all fasta seqs data, "cat Fasta/* >> allseqs.fasta"
5. cp RDPII RDPII.nhr RDPII.nin RDPII.nsq to whatever you want to be
6. /bioinfo/packages/BLAST/blast-2.2.22/bin/formatdb -i allseqs.fasta -p F
   

Run 0_start_pilot.sh

If there is no rdp file, we have to run rdp first. It is in the 0_start_pilot.sh.

First, check parse_read file and see filename and change the path.
Second, check generate_summary_table and pick right info.
third, check parse_metadata file and check "NOTE"
fourth, create a folder which is called "MSA"
fifth, check 0_start_pilot.sh and run each script
sixth, check AAG.fasta file is there or not

1. ./create_rank_result.sh
2. perl parse_metadata.pl
3. perl generate_summary_table.pl
4. sh generateTop10.sh
5. generate_gensum_gencount.pl
6. perl gen_seq_unifrac.pl
7. sh run_clustraw.sh------before run this script, cat RDP/* >> allseqs_rdp.txt

After we will see .phy files in the MSA folder, we use
/scratch/cc0430/phylip-3.69/src/dnadist and copy the filename on it and type "y"
mv outfile idealSeqs.0.6.fasta.dnadist.outfile
/scratch/cc0430/phylip-3.69/src/neighbor and take idealSeqs.0.6.fasta.dnadist.outfile and type "y"
mv outfile idealSeqs.0.6.fasta.neighbor.outfile
mv outtree idealSeqs.0.6.fasta.neighbor.outtree