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Fix typo

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barneypotter24 committed Sep 8, 2017
2 parents fa53f0a + e9c7320 commit 6bcbfcd33969b2b5e010d8a98ac2a1e5a139e319
Showing with 1 addition and 1 deletion.
  1. +1 −1 pipeline/README.md
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@@ -54,7 +54,7 @@ If this is the case, then you will need to split the files back up into smaller
##### Extract fasta files from basecalled reads and demultiplex reads based on barcoding:
1. Load Poretools with `ml nanopolish/0.7.1-foss-2016b` (Uses Python 2).
2. Change working directory to `<BASECALLED_READS_DIRECTORY>/workspace/demux/`.
3. Submit job as `sbatch --time=96:00:00 --mem=32000 --mail-type=END,FAIL --mail-user=<EMAIL_ADDRESS.org --wrap="$EBROOTNANOPOLISH/nanopolish extract -b albacore -t template -o nanopolish_full.fasta ../"`.
3. Submit job as `sbatch --time=96:00:00 --mem=32000 --mail-type=END,FAIL --mail-user=<EMAIL_ADDRESS> --wrap="$EBROOTNANOPOLISH/nanopolish extract -b albacore -t template -o nanopolish_full.fasta ../"`.
4. Load Porechop with `module load Python/3.5.2-foss-2016b-fh1` (uses Python 3).
5. Submit job as `sbatch --time=24:00:00 --mem=20000 --mail-type=END,FAIL --mail-user=<EMAIL_ADDRESS> --wrap="porechop -i <FILENAME.fasta> -b . --barcode_threshold 75 --threads 16 --check_reads 100000"`.
6. Once job completes, run `gunzip NB*` from within the directory to unzip the files in preparation for consensus genome generation.

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