Differences

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--- deconseq_for_decontaminating_reads [2017/08/24 07:43] – cgeb2001
+++ deconseq_for_decontaminating_reads [2018/06/28 15:58] (current) – 134.190.133.209
@@ Line 1: / Line 1: @@
-**DECONSEQ**
+====== DECONSEQ ======
 Documentation by Sarah Shah, Shelby Williams
@@ Line 7: / Line 8: @@
 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.
-. Make a bwa index by:
+. Make a bwa index of your contamination fasta file by:
 <code>
 bwa64 index -p prefix_of_your_choice_for_bacteria_index -a bwtsw fasta_file_of_your_suspected_bacteria >bwa.log 2>&1 &
 </code>
+You can check the status of your bwa index by using "tail -f bwa.log".
 . Move the 8 index files to the folder "db".
-. Edit the config file (DeconSeqConfig.pm) as such:
+a. Edit the config file (DeconSeqConfig.pm) as such:
 <code>
 'prefix_of_bacteria_index' => {name => 'Nameofyourchoice',
                         db => 'prefix_of_bacteria_index'},
 </code>
-Do not edit anything else.
+b. 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.
 . Write a shell script (example below) and qsub it.