Notes and code for evaluation of single cell processing tools
- STARsolo from Alex, the author or STAR.
- Kallisto + bustools, a python wrapper kb-python can be handy but the error messages are not that informative in my experience. Read the preprint: Modular and efficient pre-processing of single-cell RNA-seq
- Salmon + Alevin read the preprint: Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. It support single-nuclei data now!
(cellranger count times), source data location: /n/boslfs02/LABS/informatics/sequencing/source/
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191218_A00794_0145_AH2G23DSXY - S4 Novaseq (90 samples, we didn't finish count for this one, just delivered fastq)
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200227_A00794_0189_BH2JF2DSXY - S4 Novaseq (54 samples, approx 20hrs)
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200316_A00794_0205_AHN3N3DMXX - S2 Novaseq (7.5 hrs x 4 samples, 14 hrs x 1 sample, 13 hrs x 1 sample)
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200306_NB551608_0159_AHNNVKBGXC - Nextseq 1 sample (5 hrs)
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200316_D00742_0363_BHCVK3BCX3 - HiSeq 3 samples (3 hrs x 2 samples, 1 hr x 1 sample)