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fix: add more logging statemens to
sleuth-diffexp.R
, add QuantSeq t…
…esting data to get QuantSeq tests to pass (#86) The underlying problem that we identified with the work on this `debug-vroom` branch was a malformatted `custom` file for specifying canonical transcript to use in `sleuth-diffexp.R`. The take-away message here were: 1. The `sleuth-diffexp.R` script with its large `write_results()` function was hard to debug, and to ease the burden a bit in the future, we should probably keep the extra logging statements we included. 2. The `datavzrd/diffexp-template.yaml` does not seem to play nice with `custom` canonical transcript files. The `canonical` column does not make sense in the `genes_aggregated` results table (as this should only contain gene names / identifiers, and no transcript identifiers, and only the latter could be canonical or not), so we remove it there. However, how to have a `canonical` column in the `genes_representative` case with a `custom` canonical transcript file still needs to be solved before merging this PR.
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The testing data for this test case is downloaded from this Zenodo dataset: | ||
https://zenodo.org/doi/10.5281/zenodo.10572745 | ||
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It has been generated by this snakemake workflow: | ||
https://github.com/dlaehnemann/create-quant-seq-testing-dataset | ||
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So it is based from data from this publication: | ||
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Corley, S.M., Troy, N.M., Bosco, A. et al. QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis. Sci Rep 9, 18895 (2019). https://doi.org/10.1038/s41598-019-55434-x | ||
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The MSigDB gene sets are used according to their [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/), which is given here: | ||
https://www.gsea-msigdb.org/gsea/msigdb_license_terms.jsp |
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UROSEVIC_RESPONSE_TO_IMIQUIMOD https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/UROSEVIC_RESPONSE_TO_IMIQUIMOD BRCA1 CCL8 CXCL11 IDO1 IFI35 IFI6 IFITM1 IL6 IRF7 ISG15 ISG20 MICB MX1 OAS2 OASL PLAAT4 SECTM1 STAT1 TRAFD1 | ||
KEGG_PROTEASOME https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/KEGG_PROTEASOME IFNG POMP PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA6P4 PSMA7 PSMA8 PSMB1 PSMB10 PSMB11 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC1P4 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD6 PSMD7 PSMD8 PSME1 PSME2 PSME3 PSME4 PSMF1 SEM1 |
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sample condition | ||
SRR8309096 Control | ||
SRR8309094 Control | ||
SRR8309095 Treated | ||
SRR8309097 Treated | ||
SRR8309098 Control | ||
SRR8309099 Treated |
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sample unit fragment_len_mean fragment_len_sd fq1 fq2 | ||
SRR8309096 u1 430 43 quant_seq_test_data/SRR8309096.fastq.gz | ||
SRR8309094 u1 430 43 quant_seq_test_data/SRR8309094.fastq.gz | ||
SRR8309095 u1 430 43 quant_seq_test_data/SRR8309095.fastq.gz | ||
SRR8309097 u1 430 43 quant_seq_test_data/SRR8309097.fastq.gz | ||
SRR8309098 u1 430 43 quant_seq_test_data/SRR8309098.fastq.gz | ||
SRR8309099 u1 430 43 quant_seq_test_data/SRR8309099.fastq.gz |
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from snakemake.utils import min_version | ||
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min_version("7.17.0") | ||
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configfile: "config/config.yaml" | ||
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# declare main workflow as a module | ||
module rna_seq_kallisto_sleuth: | ||
snakefile: | ||
"../../../workflow/Snakefile" | ||
config: | ||
config | ||
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use rule * from rna_seq_kallisto_sleuth | ||
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rule download_quant_seq_testing_data: | ||
output: | ||
"quant_seq_test_data.tar.gz", | ||
log: | ||
"logs/download_quant_seq_testing_data.log", | ||
shell: | ||
"wget https://zenodo.org/records/10572746/files/quant_seq_test_data.tar.gz 2>{log} " | ||
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rule extract_quant_seq_testing_data: | ||
input: | ||
"quant_seq_test_data.tar.gz", | ||
output: | ||
"quant_seq_test_data/README.md", | ||
"quant_seq_test_data/SRR8309099.fastq.gz", | ||
"quant_seq_test_data/SRR8309095.fastq.gz", | ||
"quant_seq_test_data/SRR8309096.fastq.gz", | ||
"quant_seq_test_data/samples.tsv", | ||
"quant_seq_test_data/SRR8309097.fastq.gz", | ||
"quant_seq_test_data/SRR8309094.fastq.gz", | ||
"quant_seq_test_data/SRR8309098.fastq.gz", | ||
log: | ||
"logs/extract_quant_seq_testing_data.log", | ||
shell: | ||
"tar xzfv {input} 2>{log}" |
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