Hi,
I am using m6Anet for 4 nanopore premethion runs for directRNA sequencing. We have 4-5 million reads for each sample. When I run the m6anet dataprep, there is a parameter –readcount_max=NUM (default is 1000). I wonder if the default setting was used, for the sites with more than 1000 read covered, will only 1000 read be kept for the following analysis? Is it randomly selected 1000 reads? Since we have a lot of reads, should we increase this number? Should I set it to 5000 or even higher?
Hi, I am using m6Anet for 4 nanopore premethion runs for directRNA sequencing. We have 4-5 million reads for each sample. When I run the m6anet dataprep, there is a parameter –readcount_max=NUM (default is 1000). I wonder if the default setting was used, for the sites with more than 1000 read covered, will only 1000 read be kept for the following analysis? Is it randomly selected 1000 reads? Since we have a lot of reads, should we increase this number? Should I set it to 5000 or even higher?
Thank you!
Best, Ying