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:
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](https://user-images.githubusercontent.com/82668933/115052395-84fbb380-9efb-11eb-921c-d387c6712ec3.png)
Kindly help!
Thanks, Manasa