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deconseq_for_decontaminating_reads [2017/08/24 05:59] – cgeb2001deconseq_for_decontaminating_reads [2018/06/28 15:58] (current) – 134.190.133.209
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-**DECONSEQ**+====== DECONSEQ ====== 
  
 Documentation by Sarah Shah, Shelby Williams Documentation by Sarah Shah, Shelby Williams
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 Warning: If your read file is above 4GB, you must split it. Deconseq's Github page has also been abandoned since 2014, so do not expect an update or a fix for a bug. Warning: If your read file is above 4GB, you must split it. Deconseq's Github page has also been abandoned since 2014, so do not expect an update or a fix for a bug.
  
-This can be used to decontaminate reads using a database of your suspected contaminant sequences. I recommend using this for fine-combing through data that doesn't have much contaminants to begin with. +This can be used to decontaminate reads using a database of your suspected contaminant sequences. To start, create a fasta file with genomes of suspected contaminates. I recommend using this for fine-combing through data that doesn't have much contaminants to begin with. 
  
-1. Make a bwa index by:+1. Make a bwa index of your contamination fasta file by:
 <code> <code>
 bwa64 index -p prefix_of_your_choice_for_bacteria_index -a bwtsw fasta_file_of_your_suspected_bacteria >bwa.log 2>&1 & bwa64 index -p prefix_of_your_choice_for_bacteria_index -a bwtsw fasta_file_of_your_suspected_bacteria >bwa.log 2>&1 &
 </code> </code>
 +
 +You can check the status of your bwa index by using "tail -f bwa.log".
  
 2. Move the 8 index files to the folder "db". 2. Move the 8 index files to the folder "db".
  
-3. Edit the config file (DeconSeqConfig.pm) as such:+3a. Edit the config file (DeconSeqConfig.pm) as such:
 <code> <code>
-bact => {name => 'Nameofyourchoice',  +'prefix_of_bacteria_index' => {name => 'Nameofyourchoice',  
-           db => 'prefix_of_bacteria_index'},+                        db => 'prefix_of_bacteria_index'},
 </code> </code>
-Do not edit anything else.+ 
 +3b. Also edit the following lines in the config file: 
 +<code> 
 +use constant DB_DIR => '/path/to/deconseq/db/'; 
 +use constant PROG_DIR => '/path/to/deconseq/'; 
 +</code> 
 + 
 +This is because of a bug (see https://www.biostars.org/p/182337/). Do not edit anything else.
  
 4. Write a shell script (example below) and qsub it. 4. Write a shell script (example below) and qsub it.
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 #$ -cwd #$ -cwd
  
-perl deconseq.pl -f Blasto_filtered.fastq -dbs prefix_of_bacteria_index -out_dir outfolder -keep_tmp_files -i 85  -id testdeconseq+perl deconseq.pl -f Read_file_to_decontaminate.fastq -dbs prefix_of_bacteria_index -out_dir outfolder -keep_tmp_files -i 85  -id testdeconseq
 </code> </code>
  
deconseq_for_decontaminating_reads.1503565178.txt.gz · Last modified: by cgeb2001