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Misc other features
Caleb Lareau edited this page Jul 25, 2019
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We note that this modality is not officially supported but may still be useful nonetheless.
The bap-frag module was written as the original implementation of bap did not output frag files. If you want frag files for a newly analyzed dataset, run bap2 as this provides an automatic generation of these files.
The only time bap-frag should be used is reanalyzing already-processed data with bap. An example execution of this is shown here:
bap-frag -i data/jaccardPairsForIGV.bam -be for_frag/jaccardPairsForIGV.barcodeTranslate.tsv -o frag_bap_test -z
Please raise an issue here