cjprybol / neurospora_bsa_mutation_mapper Goto Github PK
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License: MIT License
right now it's static in the lighter and bowtie scripts.
suggested fix: make the number of cores dynamically callable from the parents.txt file
consider renaming the parents.txt file, to reflect that it's a config file
can wrap the single end and paired end scripts in 010 and 020 in if-else statements that reflect whatever is specified in the confit.txt file
for
also, edit the min and max fragment size of the input library in the
ESSENTIAL/SCRIPTS/021.paired_end_map_to_OR.sh
file for the bowtie2 mapping command (line 65)
develop with this method. After sequencing Mauriceville strain next session, update to use that
Its on the cluster @
/usr/local/samtools/latest/wgsim
Make sure to use it without allowing any errors using these options:
-e 0 -r 0 -R 0 -X 0 -s 0
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