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MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
MIT License
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NoDataError: empty CSV #93

Open peipp410 opened 3 months ago

peipp410 commented 3 months ago

Hello! I encountered the following error. I tried to check the source code but I can't locate where the function is because there is no file called 'oligo_filter.py'. What's the possible cause of this error and how to fix that? Thanks! WechatIMG2977

lishuangshuang0616 commented 3 months ago

Can you check the results in 01.data/oligo.sequencing.report.csv and also provide the screenshot of the results from 01.data/oligo.reads.fq.gz?

peipp410 commented 3 months ago

29901723521993_ pic_hd None of the reads passed QC, which is so wired. The fastq file is also empty. How could that happen?

peipp410 commented 3 months ago

p.s. with arguments "--chemistry scRNAv2HT --darkreaction unset,unset"

lishuangshuang0616 commented 3 months ago

Screenshot the first 10 sequences R1/R2 of cDNA and oligo, I'll take a look

peipp410 commented 3 months ago

552a16b5eb225d30ccb124e835663225 Thanks! Problem solved. 'N'-base exists.

lishuangshuang0616 commented 3 months ago

Yes, this version will cause reads to be filtered for oligo fastq containing N. Currently, you can only manually remove the fixed sequence. This problem will be solved in the upcoming 2.1.3 version.