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***`all_splicing_variants*.bed`** - a file containing all of the variants that regtools identified as being associated with a junction for the given parameters used to run `cis-splice-effects identify`.
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***`dir_names.tsv`** - a file containing a list of each of the sample directories with each directory on a new line. This can be obtained by using `ls samples/ > dir_names.tsv`. For this example, it would look like:
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-
```bash
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Sample_1
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Sample_2
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```
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```bash
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Sample_1
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+
Sample_2
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```
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***`variants_all_sorted.vcf.gz`** - a compressed vcf file containing all variants from all samples.
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***`variants_all_sorted.vcf.gz.tbi`** - an index file for the vcf file mentioned above.
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