Differences

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--- short_read_assembly [2019/09/06 12:32] – created 134.190.234.196
+++ short_read_assembly [2019/09/09 08:17] (current) – 24.138.68.92
@@ Line 7: / Line 7: @@
 #$ -cwd\\
 #$ -o Blah.log\\
-#$ -pe threaded 21\\
+#$ -pe threaded 20\\
-source activate spades\\
-##
-metaspades.py -t 20 -m 230 --pe1-1 Blah_R1_PairNtrim.fq --pe1-2 Blah_R2_PairNtrim.fq  --pe1-s Blah_R1_unPairNtrim.fq --pe2-s Blah_R2_unPairNtrim.fq -o Metaspades_Blah_output\\
-##
+cd /to/the/path/containing/the reads/\\
+source activate spades\\
+metaspades.py -t 20 -m 230 --pe1-1 Blah_R1_PairNtrim.fq --pe1-2 Blah_R2_PairNtrim.fq  --pe-s Blah_R1R2unPairNtrim.fq -o /path/to/Metaspades_Blah_output\\
 conda deactivate