Hello,
I'm a master's student and a newbie in bioinformatics studies. I scanned my nanopore sequence data with ISEScan to see how many IS elements I have in the reads (it has long and short reads but long reads are more important). After that, I annotated the sequences using PGAP (NCBI's prokaryotic genome annotation pipeline), and most IS elements obtained by ISEScan needed to match the PGAP results. However, there are some overestimated results in my ISEScan reports when I compared with PGAP results. PGAP is a strong tool; other annotation results look consistent since I used it with my reference genome. However, I need a proper IS elements report, that's why I used ISEScan. ISEScan was suggested by my colleague, and it seems like a powerful tool. I feel like I did something wrong. Can you help me how to solve it?
Hello, I'm a master's student and a newbie in bioinformatics studies. I scanned my nanopore sequence data with ISEScan to see how many IS elements I have in the reads (it has long and short reads but long reads are more important). After that, I annotated the sequences using PGAP (NCBI's prokaryotic genome annotation pipeline), and most IS elements obtained by ISEScan needed to match the PGAP results. However, there are some overestimated results in my ISEScan reports when I compared with PGAP results. PGAP is a strong tool; other annotation results look consistent since I used it with my reference genome. However, I need a proper IS elements report, that's why I used ISEScan. ISEScan was suggested by my colleague, and it seems like a powerful tool. I feel like I did something wrong. Can you help me how to solve it?