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Cell ranger count gtf parsing SOS

Hi

I have been trying to run cellranger count on customized reference, which I constructed using NCBI downloaded reference genome and gtf annotation via cellranger mkref. However, it is reporting "[error] Pipestance failed. Error parsing GTF on line:" , and when I looked at that specific line it looked like that line is missing transcript id info.

I would highly appreciate any thought or suggestions to solve this. Thanks in advance!

rna-seq
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written by linzhangucla • linzhangucla

Could you please specify which GTF file this is and how you have downloaded it?

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written by vkkodali_ncbi vkkodali_ncbi

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