Differences

This shows you the differences between two versions of the page.

--- ploidy_analysis_using_ploidyngs [2022/06/24 15:56] – 134.190.232.29
+++ ploidy_analysis_using_ploidyngs [2022/06/24 16:01] (current) – [UPDATE (June 2022)] 134.190.232.29
@@ Line 77: / Line 77: @@
   * The axis titles in the histogram will be a bit easier to understand
   * The script will now report the total number of heteromorphic positions per contig and over all contigs
+To call it, use a Perun submission script like this one
+<code>
+#!/bin/bash
+#$ -S /bin/bash
+. /etc/profile
+#$ -cwd
+#$ -q 256G-batch
+source activate ploidyNGS-dependencies
+export PATH="/scratch2/software/ploidyNGS:$PATH"
+BAMFILE='dnaseq_vs_canu_ergo_assembly.sorted.bam'
+MINCOV=10
+MAXDEPTH=2000
+OUTBASE='dnaseq_vs_canu_ergo_assembly'
+ploidyNGS_minCov.py \
+    --out $OUTBASE \
+    --bam $BAMFILE \
+    --min_cov $MINCOV \
+    --max_depth $MAXDEPTH
+conda deactivate
+</code>
+A more elaborate script is available on the GitHub repository of the Roger lab: https://github.com/RogerLab/gospel_of_andrew.
+The updated scripts are also available on the original GitHub repository https://github.com/diriano/ploidyNGS under the original script names ''ploidyNGS.py'' and ''ploidyNGS_generateHistogram.R''