Tophat's defaults sets: --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2.
This gave me about 4% alignment for mm9 mouse data.
I tried up to --read-mismatches 30 --read-gap-length 30 --read-edit-dist 30. This gave me 20.9% alignment.
The reads are 150 bp long. What are the proper settings for such long reads? If I wanted to use tophat, rather than other tools that may be better suited for long reads, what would I need to take into consideration? Any other parameters?
This gave me about 4% alignment for mm9 mouse data.
I tried up to --read-mismatches 30 --read-gap-length 30 --read-edit-dist 30. This gave me 20.9% alignment.
The reads are 150 bp long. What are the proper settings for such long reads? If I wanted to use tophat, rather than other tools that may be better suited for long reads, what would I need to take into consideration? Any other parameters?
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