Scripts used to extract lox-derived deletions.
The example described here allows to reproduce the results observed in 'LoxTnSeq: Transposon mutagenesis coupled with ultra sequencing to study large random genome reductions' by Daniel Shaw et al. (to be published).
Python3, blast command line tool
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Locate all fastq files in the same directory with the scripts from this repository.
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Run peFastq2LoxDel to generate the blast files from the raw paired-end fastq:
python3 peFastq2LoxDel.py
User can change the inverted repeat to detect, the genome and blast settings directly in that script. As alternative, seFastq2LoxDel process the paired reads separatedly to detect inverted repeats and then pastes the sequences, allowing for extra coverage but also, in our experience, a lot of off-target signals.
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Filter the blast file to take those reads covering a deletion point:
3.1) Edit Blast2LoxDel with the file of interest to process and run:
python3 Blast2LoxDel.py
3.2) Alternatively and preferred, this step is thought to be performed in a python environment importing the function filter_deletions from this script.