Closed CadenZhao closed 3 years ago
BTW, software version: cellranger 4.0.0
@CadenZhao I wondered if you got any response from 10x to this issue as I got the same error message for several samples recently. Thanks! Kimia
Please contact support@10xgenomics.com for help with this issue.
@CadenZhao @evolvedmicrobe @dadkhahk i wonder if you got any response from 10X to this issue as i got the same error message. Thinks! longrw
Not here. 10x usually doesn't respond here and they are more responsive through email. They will ask for some files to be provided so they can figure out the issue: support@10xgenomics.com
In order to distinguish between the 3' vs 5' assay configuration the following conditions need to be satisfied:
- A minimum of 1000 confidently mapped reads
- A minimum of 5.0% of the total reads considered needs to be confidently mapped
- The number of sense reads need to be at least 2x compared to the antisense reads or vice versa
Please validate the inputs and/or specify the chemistry via the --chemistry argument.
Fastqs downloaded from SRA:![image](https://user-images.githubusercontent.com/30337666/92454913-9e18e500-f1f3-11ea-9f81-ddcba11fe582.png)
My shell scripts to iteratively run cellranger count:
ERROR I got:![image](https://user-images.githubusercontent.com/30337666/92454278-eaaff080-f1f2-11ea-924e-0a307b3791e1.png)
Among 14 samples, 7 can be processed successfully:![image](https://user-images.githubusercontent.com/30337666/92456297-4f6c4a80-f1f5-11ea-872b-e5690fede598.png)
One ERROR is different from others:
I fount this file size is different from the file in SRA, I'll re-download it.
But file sizes in the other 6 ERRORs are same as files in SRA. How should I debug it?
Thank you very much!