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