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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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Error with Smart-seq2 dataset #269

Closed juicejulia closed 3 years ago

juicejulia commented 3 years ago

Hi there, thank you for creating such a powerful and flexible tool. I have received a smart-seq2 datasets with reads already demultiplexed. I have followed the wiki procedure to generate concatenated reads and pseudobarcode files. However, when I execute zUMIs filtering step, I encountered the following error:

You provided these parameters: YAML file: Smart-seq2_zUMIs.yaml zUMIs directory: /home/jwang/software/zUMIs STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: 0 zUMIs version 2.9.6

[1] " reads were assigned to barcodes that do not correspond to intact cells." Error in setnames(x, value) : Can't assign 0 names to a 1 column data.table Calls: BCbin ... colnames<- -> names<- -> names<-.data.table -> setnames Execution halted

My yaml file attached here. Could you help? Thank you! Smart-seq2_zUMIs.yaml.txt

cziegenhain commented 3 years ago

Hi,

I think this issue could arise from attempting to error correct on the barcode (BarcodeBinning: 1) because all reads with their pseudo barcodes all fit perfectly to the expectation! Could you please retry with BarcodeBinning: 0?

juicejulia commented 3 years ago

The pipeline runs with no issues after changing the Binning to 0. Thank you Christoph!

cziegenhain commented 3 years ago

Great, I'll make some changes to prevent this problem in the next update.