Entering edit mode
12.2 years ago
Zhlingl
•
0
hello, i am using GBrowse to display NGS data, and i want to show the gene expression profiling which calculated the sum of reads abundance in each loci and show it on browse, i have tried the coverage feature and the results are quite like the profiling shows, however, it counts the sum of unique reads number instead of the total abundance of reads, for example one read sequenced for 1000 times but in the browser it only show one time, it is not what i want. Anybody can help me whit that?
many thanks and best wishes!
didn't quite get your point, why abundance is not what is shown with feature 'coverage'? and what does it mean 'one read sequenced 1000 times'?
Sorry, my expression is not clear. Because the reads are non-redundancy. for example, read1 may have 1000 copies in the raw file, but in the non-redundancy file it appears only 1 time with the abundance feature of 1000, so the unique number is 1 and the total number is 1000.Therefore, the unique number and total number of reads have different meanings. the coverage feature only reflect the situation of unique reads number, and i want to show total reads number. did i make the expression more clearly?
What is 'redundancy'? Are they identical duplicates due to PCR enrichment before sequencing? I think it depends on how you process the bam alignment files, whether you remove these duplicates or not. If you don't, gbrowse will visualize the duplicates.