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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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Failed to open filtered.tagged.unmapped.bam #379

Open aduntslusine opened 8 months ago

aduntslusine commented 8 months ago

Initially, I had demultiplexed Smart-Seq 3 dataset for each cell separately without barcodes. I concatenated 5 fastq files with this tool. It creates artificial barcodes that can be used in yaml. I started the analysis with mapping step and got the following error:

Failed to open file /storage2/users/lusine/hepatocyte_maturation/zUMIs_out_with_barcode_r1/Smartseq3_hepatocyte_maturation.filtered.tagged.unmapped.bam samtools view: failed to open "/storage2/users/lusine/hepatocyte_maturation/zUMIs_out_with_barcode_r1/Smartseq3_hepatocyte_maturation.filtered.tagged.unmapped.bam" for reading: No such file or directory

The yaml file, the output and log file can be found here.

Apparently the unmapped bam file is not created and I cannot find out why. Any help will be much appreciated.

cziegenhain commented 8 months ago

Hi!

Did you try to start the pipeline from "Filtering"? That should be the first step, even when you start from concatenated files. Your YAML config file looks OK otherwise.

Best, Christoph