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Update README.md
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e-sollier authored Oct 29, 2024
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Expand Up @@ -22,7 +22,7 @@ The fields chr2 and pos2 are optional (for example if you only have copy number
A bed file of topologically-associating domains can be used, in which case only the breakpoints in the same TAD as a gene are considered in the search for enhancer hijacking events. One TAD file is provided in the data directory. If not TAD file is provided, pyjacker will instead look for breakpoints within a fixed distance to the gene (1.5Mb by default). See data/HSPC_TADs.bed for an example.

### Allelic read counts at SNPs in RNAseq (optional)
This is used to detect monoallelic expression. This requires files generated by GATK ASEReadCounter.
This is used to detect monoallelic expression. This requires files generated by [fast_ase](https://github.com/e-sollier/fast_ase) or [GATK ASEReadCounter](https://gatk.broadinstitute.org/hc/en-us/articles/360037428291-ASEReadCounter).

### Copy number alterations (optional)
tsv file with the following columns: sample, chr, start, end, cn. See data/CNAs.tsv for an example.
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