Comments (1)
grst
commented on June 28, 2024
How would the samplesheet look like in this case? Since with smartseq every cell is sequenced independently, wouldn't this lead to one sample per cell in the end? We likely would need a different logic for merging biological samples in that case.
In the past we have recommended to use the rnaseq pipeline for smart-seq2 data. Is there any reason why this doesn't work for you?
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Related Issues (20)
- Switch to use central nf-core modules
- Autorenaming of files in new cellranger module leads to erroneous renaming of sample ID containing R1 in it, like in SRR ids HOT 2
- Multi-omics support (meta-issue) HOT 3
- exceeded running time limit (8h) HOT 3
- Crash when specifying existing --star_index using star aligner HOT 6
- Bump up kb to 0.28.0 HOT 3
- Use nf-validation plugin HOT 1
- Update or remove universc HOT 8
- Tests for cellranger-arc HOT 1
- MuData conversion
- Utilize central modules for simpleaf workflow HOT 1
- The cellrangerarc cannot start successfully HOT 2
- When aligner is cellrangerarc the step MTX_TO_SEURAT failed HOT 3
- Avoid error on unknown headers in input.csv HOT 4
- Issues with samplesheet.csv as well as additional columns in the samplesheet HOT 3
- Samplesheet Check Bug HOT 1
- Flexible input read format with STARsolo with --soloBarcodeReadLength HOT 1
- Make scrnaseq pipeline v2.5.1 compatible with nextflow v22.04.0 HOT 1
- Clean up mtx conversion code
- Update to the latest simpleaf HOT 3
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