Comments (5)
If the values are 'yes' or 'reverse' then yes. If some samples were sequenced not strand-specifically, then no.
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The problem is that GTEX control samples are STRAND = no. Does that mean I cannot use them together with my samples that are STRAND = yes?
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And if the above is not possible, do you have any suggestions for what to do?
from drop.
And just to clarify - what I mean is not whether it is recommended to combine stranded with unstranded samples -- I know that is not recommended.
The question is if the pipeline will run at all when combining samples with different STRAND annotations.
from drop.
Yes, you can run the pipeline with different strand options, as they are defined for each sample individually. This might lead to batch effects that might or might not be corrected well by the autoencoder. You could either count your samples in a strand unspecific mode or count them strand specifically and evaluate based on the heatmap in the outrider summary, how strong the batch effect is. We would recommend the former, as it minimises known effects.
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Related Issues (20)
- Running pipeline offline in trusted research environemnt HOT 1
- lymphoblastoid cell lines datasets of gene counts
- Error running aberrantSplicing HOT 2
- Error in AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R HOT 3
- Error in MAE QC create matrix dna rna cor HOT 3
- CalledProcessError in installRPackages.R HOT 5
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- Chunk options `#+echo` not correctly parsed HOT 1
- Incompatible with `Snakemake>=8` HOT 2
- Writing `rds` files as log can crash Snakemake execution HOT 1
- Error in h(simpleError(msg, call)) HOT 8
- requirementsR.txt referencing HEAD leads to irreproducibility / pipeline breaking HOT 3
- Problem running DROP HOT 2
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- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 10
- Pipeline fails with no significant results (AberrantSplicing_pipeline_FRASER_08_extract_results_FraseR_R) HOT 1
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 2
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- useNames = NA is defunct HOT 4
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