Hello everyone,
1. I used STAR for mapping RNA seq data with default parameters only changing --outFilterMismatchNmax 5 (allowing 5 mismatches, default was 10). I am now confused if I should have gone for 3 or less? My read length varies between 10-50. What is the ideal cutoff one should allow for mismatch parameter?
2. Also, one should go for multi-mapping reads or not? because around 24% of reads in my case is showing multi-mapping, is it significant? i don't think so.. should I switch it to zero multi-mapping?
3. I also want to do some statistics to see the correlation between my replicates, and some post-mapping statistical analysis like length counts, log(n) etc..can anybody refer a good tool for this..?
Please suggest. thanks.
1. I used STAR for mapping RNA seq data with default parameters only changing --outFilterMismatchNmax 5 (allowing 5 mismatches, default was 10). I am now confused if I should have gone for 3 or less? My read length varies between 10-50. What is the ideal cutoff one should allow for mismatch parameter?
2. Also, one should go for multi-mapping reads or not? because around 24% of reads in my case is showing multi-mapping, is it significant? i don't think so.. should I switch it to zero multi-mapping?
3. I also want to do some statistics to see the correlation between my replicates, and some post-mapping statistical analysis like length counts, log(n) etc..can anybody refer a good tool for this..?
Please suggest. thanks.
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