uoflbioinformatics/seekcrit

seek for circular RNA in transcriptome (tool to identify deferentially expressed circRNAs between two samples)

seekcrit's Issues

Requirement of file even when the file is provided

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 :

Kindly help!

Thanks,
Manasa

Aligners

Dear seekCRIT-team,

will there be an option available to use other aligners as well, like HISAT2 or something similar?

Thanks and all the best,
Danny.

Error in code

Hello !
I'm new to using this tool. After using the command., An exception keeps raising. Kindly look into it.
This is the command used.
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:

kindly help.
thanks,
manasa