Zuyao Liu

@sagnikbanerjee15 I have been trying to debug the script removeSpuriousTranscriptsBasedOnCDS.py. For me, everything looks fine so far. But the filtration on repeat doesn't work at all. I tried to change...

> Hmm, Not sure why it would not work. Did you remove the files and try again? `finder` by default will skip files that are already present to prevent taking...

@sagnikbanerjee15 I rerun the pipeline, and the genes in repetitive regions seem still to be not removed. Here is the file size. The file size with total genes that are...

Hi @sagnikbanerjee15 Here are the results. For combined_with_CDS.gtf: 84761 For combined_with_CDS_high_conf.gtf: 83365 For combined_with_CDS_low.gtf: 3986 I sorted the attributes column based on the gene_id and removed the redundancy, excluding the...

Hi @sagnikbanerjee15 I upload the files to Google drive. Here is the link: https://drive.google.com/file/d/1z37gEJSP1mLMIQrE5LlB5WITLFhkqeBZ/view?usp=sharing For testing, I upload one chromosome fasta file , meta.csv, gtf files in the screensot and...