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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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Issues while starting zUMIs #383

Open Thomas-Michiels opened 9 months ago

Thomas-Michiels commented 9 months ago

Hi,

I'm having issues while starting zUMIs. I downloaded the PBMC data from the Smartseq3Express paper (https://www.nature.com/articles/s41587-022-01311-4) to test the zUMIs pipeline. I demultiplexed the files using the zUMIs demultiplex function. Afterwards I created the yaml file for the reads and indexes. However, when trying to run zUMIs I encounter the following error: "Using miniconda environment for zUMIs! note: internal executables will be used instead of those specified in the YAML file! YAML file has an error. Look at the zUMIs_YAMLerror.log or contact developers.". When I open the error.log file I get the following output: "1". Do you know what is wrong with my YAML file that could cause this error?

Thank you in advance!

Kind regards,

Thomas

SS3_test_zUMIs.txt

cziegenhain commented 9 months ago

Hi,

For zUMIs to work, you dont necessarily need to demultiplex the files first (and then merge them again) . Other than that, try to modify as follows:

In file 3, you miss the key base_definition: If I remember correctly, the random generated barcodes when merging previously demultiplexed fastq are 8 bp, so try BC(1-8)

All the best, Christoph