Closed zjwang6 closed 2 years ago
Should be ok, I last updated the example run 2 years ago so probably an older version of STAR and many other changes since then.
Thank you for your reply. I took a carefully look, and found the gff file only has infomation of one chromosome.
Hello, My data is obtained through the smart-seq3 method, one data per cell, do not need barcode. In this case, how to set the parameters. Hope to get your guidance, thank you very much.
it is best to start with data that has not been demultiplexed. if you only have the data as 1 set of fastq per cells, follow this guide: https://github.com/sdparekh/zUMIs/wiki/Starting-from-demultiplexed-fastq-files
Hello, Dear author, I try to use zUMI to process my own smart-seq3 data, and recombine fastq files and generate an arbitrary index sequence. But I still got a bug. Next is the file of err report and yaml. zumi.err.txt runExample1.yaml.txt
I try to find the reason of bug, I found the problem occur in script of barcodeIDFUN.R. But i do not know why. Can you give me some advice. Thank you.
Since the arbitrary barcodes will all perfectly match, simply set BarcodeBinning: 0.
Best, Christoph
Thank you very much for your prompt reply
Best wishes
Hello, I use the offering example data, but the result is not same to yours. And it not report any eroor. follow is the file of Example.filtered.tagged.Log.final.out and runExample1.yaml ` Started job on | Aug 31 17:35:07 Started mapping on | Aug 31 17:35:11 Finished on | Aug 31 17:37:11 Mapping speed, Million of reads per hour | 25.60
Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Example.filtered.tagged.Log.final.out...skipping... Started job on | Aug 31 17:35:07 Started mapping on | Aug 31 17:35:11 Finished on | Aug 31 17:37:11 Mapping speed, Million of reads per hour | 25.60
Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Number of reads unmapped: too short | 643952 % of reads unmapped: too short | 75.47% Number of reads unmapped: other | 456 % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
project: Example sequence_files: file1: name: /public/home/***/biosoft/scrna-seq/zUMIs/zUMIs/sample_20210831/barcoderead_HEK.1mio.fq.gz base_definition:
can you give me some advice about the difference of the result. thank you.