scRNA-Seq-TCC-prep

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kallisto transcriptome website is down

2

Hi, I am following the getting started tutorial (http://pachterlab.github.io/kallisto/10xstarting.html) for single cell RNAseq but when I get to the point: Download the “human-mouse” transcriptome from the kallisto transcriptome website. I...

alfonsosaera

Code outdated

6

Hi, I am willing to try your code for a 10x scRNA-Seq analysis. However, in the latest V2 chemistry, they changed the design of barcodes, R1 and R2 reads. In...

yingzhang121

Very low number of cells detected

2

Hi, I'm confused by this output of the first script: get_cell_barcodes.py ``` ... NUMBER_OF_SEQUENCED_BARCODES = 35910128 Detecting Cells... NUM_OF_DISTINCT_BARCODES = 5309260 CELL_WINDOW: [100, 5000] Cell_barcodes_detected: 100 NUM_OF_READS_in_CELL_BARCODES = 3200555 Calculating...

maximilianh

By default Pool() will use all available CPUs. I changed it to use NUM_THREADS from the config file.

jamestwebber