-bwa-algargument, allowing the user to specify
-replicon-idargument to specify names for the replicons if multiple reference genomes given (respective order to order appearing in reference genome(s)
python2 src/tpp.py -himar1 -bwa /usr/bin/bwa -bwa-alg aln -ref MAC109_genome.fa -replicon-id CP029332 CP029333 CP029334 -reads1 ../HJKK5BCX2_ATGCTG_1.fastq -reads2 ../HJKK5BCX2_ATGCTG_2.fastq -primer AACCTGTTA -mismatches 2 -window-size 6 -output tpp_output/avium
-himar1specifies that the Himar1 transposon was used in the transposon mutagenesis procedure. Tn5 is also supported (
-bwaspecifies the path to the
alnis widely considered obselete to
memfor reads of length > 70bp.
-refspecifies the reference genome(s) in FASTA format to which reads will be mapped. If more than one, they can be specified in either multiple FASTAs, or as a multilined FASTA (or a combination of both).
-replicon-id [contig1 contig2 ...]specifies the names of the contigs in the genome(s). These are used as filename suffixes for output files (ie *_contig1.wig, *_contig2.wig, etc). The order of the contigs is assumed to be the same as they appear in the reference genome(s) (as given with
-ref). Specifying this option is only required if there is more than one contig. Note: While you can technically use any contig name at this step, if you wish to use
wig_gb_to_csv.pyto organize the data you should use the contig names as they appear in the Genbank file (as specified by
-reads1specifies the file containing the raw reads (untrimmed) for read1 in FASTQ or FASTA format
-reads2specifies the file containing the raw reads (untrimmed) for read2 in FASTQ or FASTA format
-primerspecifies a nucleotide sequence at the end of the transposon, is used to separate transposon DNA from genomic DNA in read 1.
-window-sizespecifies how many positions to look for
-primerwithin read 1. It should be set to at least the difference between the maximum and minumum expected positions of the first base of genomic DNA in read 1 (and larger if you want to allow for insertions/deletions). For the Long et al 2015 protocol (using a pool of 4 shifting prefixes) the window-size should be at least 6. Default value is 6.
-mismatchesspecifies the number of mismatches to allow when searching for the transposon in read 1 (ie number of mismatches to
-outputspecifies the filename prefix to be applied to output files. Can include directories, allowing custom paths to be specified.
- Fixed crash in TPP. - Misc changes for outputs.