Differences

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--- deconseq_for_decontaminating_reads [2017/08/23 12:52] – 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 5: / Line 6: @@
 Source: [[http://deconseq.sourceforge.net/manual.html]] On perun: /opt/perun/deconseq-standalone-0.4.3 (copy this folder into your working directory)
-Warning: If your read file is above 4GB, you must split it.
+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.
+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>
-bact => {name => 'Nameofyourchoice', db => 'prefix_of_bacteria_index'},
+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>
-Do not edit anything else.
+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.
+<code>
 #!/bin/sh
 #$ -S /bin/sh
 . /etc/profile
 #$ -cwd
-perl deconseq.pl -f Blasto_filtered.fastq -dbs bact -out_dir outfolder -keep_tmp_files -i 85  -id testdeconseq
-The "-f" is your read file, the "-i" is how identical your sequences must be to the bacteria to be thrown out, and the "-id" is a prefix of your choice that will be added to your output read files.
+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>
+The "-f" is your read file, the "-i" is how identical your sequences must be to the bacteria to be thrown out, and the "-id" is a prefix of your choice that will be added to the names of your output read files. The "-dbs" is the handle of your index files.
 . Your shell script's error file should have a log of the number of sequences it is reading.
-. Your output folder should have:
+. Your output folder should have: one "clean" reads file, one "contaminant" reads file, and a .tsv file of alignments between your read sequences and bacterial sequences.