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UofLBioinformatics / seekCRIT

seek for circular RNA in transcriptome (tool to identify deferentially expressed circRNAs between two samples)
MIT License
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Requirement of file even when the file is provided #1

Closed maanzaa closed 3 years ago

maanzaa commented 3 years ago

Hello ! I am quite new to using seekCRIT. I want to check the expression of my circRNAs using RNA seq. I have given all the required arguments in the command but it keeps throwing error. I have included the gtf file, but then the program asks me to include gtf file. The command used is:

python3 seekCRIT.py -o AC16_PEtest -t PE -fa /STORAGE/softwares/seekCRIT/genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa --genomeIndex /STORAGE/softwares/seekCRIT/hg38_index -s1 /STORAGE/softwares/seekCRIT/circrna_ac16/AC16_RNA_Doxo_1.fastq:/STORAGE/softwares/seekCRIT/circrna_ac16/AC16_RNA_Doxo_2.fastq -s2 /STORAGE/softwares/seekCRIT/circrna_ac16/AC16_RNA_1.fastq:/STORAGE/softwares/seekCRIT/circrna_ac16/AC16_RNA_2.fastq --gtf/STORAGE/softwares/seekCRIT/genome/Homo_sapiens.GRCh38.99.gtf --threadNumber 20

The error is : Screenshot from 2021-04-16 21-32-00

Kindly help!

Thanks, Manasa

bluebear94 commented 3 years ago

It seems you forgot to put a space after --gtf. Since you've opened another issue where you fixed this, I'm going to close this one if you don't mind.