Wildcards Snakemake using bedtools
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3 months ago
Fadwa ▴ 10

Hi everyone, I need your help resolving this problem.

I'm working on diploide chromosome, and each chromosome has 2 haplotypes.

To run my snakemake, i started with two repertoire containing:

- Haplotype:
     * chr_1.gff
     * chr_2.gff
  • NLR-annotator:
    *chr_1.gff
    *chr_2.gff
    

i need to run Bedtools to intersect Chr_1.gff in Haplotype with Chr_1.gff in NLR-annotator. The problem is that generate two output, chr_1 [haplotype] vs chr_1[NLR-Annotator] and chr1_[haplotype] vs chr_2 [NLR-Annotatr]. i need only the intersection when the filenames match together.

I used wildcards but it doesn't work.

Thank you in advance

Bedtools Snakemake Wildcards • 160 views
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