TRANSIT-TPP(1) | User Commands | TRANSIT-TPP(1) |
transit-tpp - statistical calculations of essentiality of genes or genomic regions
usage: python PATH/src/tpp.py -bwa <EXECUTABLE_WITH_PATH> -ref <fasta-file|comma_separated_list> -reads1 <FASTQ_OR_FASTA_FILE> [-reads2 <FASTQ_OR_FASTA_FILE>] -output <BASE_FILENAME> [OPTIONAL ARGS]
-protocol [Sassetti|Tn5|Mme1] # which sample prep protocol was used?; sassetti protocol is the default; this sets the default transposon and primer sequence
-maxreads <INT>
-primer-start-window INT,INT # position in read to search for start of primer; default is [0,20]
-barseq_catalog_in|-barseq_catalog_out <file>
August 2020 | transit-tpp 3.1.0 |