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LSTrAP/data.template.ini
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| [GLOBAL] | |
| ; add all genomes, use semi-colons to separate multiple cfr. zma;ath | |
| genomes=zma | |
| ; enter email to receive status updates from the cluster | |
| ; setting the email to None will disable this | |
| ; Warning: this might generate a lot of emails for large datasets. Leaving this on None is recommended | |
| email=None | |
| ; orthofinder settings (runs on all species) | |
| orthofinder_output=./output/orthofinder | |
| [zma] | |
| cds_fasta= | |
| protein_fasta= | |
| genome_fasta= | |
| gff_file= | |
| gff_feature=CDS | |
| gff_id=Parent | |
| fastq_dir=./data/zma/fastq | |
| tophat_cutoff=65 | |
| htseq_cutoff=40 | |
| indexing_output=./output/bowtie-build/zma | |
| trimmomatic_output=./output/trimmed_fastq/zma | |
| alignment_output=./tmp/tophat/zma | |
| htseq_output=./output/htseq/zma | |
| exp_matrix_output=./output/zma/exp_matrix.txt | |
| exp_matrix_tpm_output=./output/zma/exp_matrix.tpm.txt | |
| exp_matrix_rpkm_output=./output/zma/exp_matrix.rpkm.txt | |
| interpro_output=./output/interpro/zma | |
| pcc_output=./output/zma/pcc.std.txt | |
| pcc_mcl_output=./output/zma/pcc.mcl.txt | |
| mcl_cluster_output=./output/zma/mcl.clusters.txt | |