Hi, I'm quite new to scRNA-seq and I got an error as below while trying to run cellranger (version 7.2.0) for public human brain cortex data.
[error] Pipestance failed. Error log at: FL/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u731a5891c0/_errors Log message: An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input: Sample FL in "path/to/FL/fastq/files". Please check your input data. - 0.1% for chemistry SC3Pv3 - 0.1% for chemistry SC3Pv3HT - 0.0% for chemistry SC5P-PE - 0.0% for chemistry SC3Pv2 - 0.0% for chemistry SC3Pv3LT Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure.
The public data I used was PRJNA491456 (included only paired end datas for my analysis) and I'm sure they are all single cell RNA-seq data, and pretty sure they are all 10x data (metadata says they are prepared from Illumina HiSeq 4000). I've searched some posts related with my problem but most of the problems happened because of different library preparation method and also this data is not multiome data (https://kb.10xgenomics.com/hc/en-us/articles/17959105349389-How-can-I-analyze-only-my-Multiome-Gene-Expression-library-with-Cell-Ranger-on-10x-Genomics-Cloud-Analysis-). When I ran cellranger with another public dataset from Illumina 10x 3' it worked well, so I think this problem SHOULD be related with library prep things and finding appropriate chemistry (if this data is not from 10x) will help my problem... Any help will be appreciated!
+) input datas format are like as below;
+) it seems all the runs are from individual sample (all of the runs had different sample code) but if the runs originate from the same brain region, I grouped them together by my mind and used as input for cellranger