Blosberg
commented
6 years ago The problem was a parsing error in Rstudios read.csv() so the pipeline is fine, but there's something else weird going on in Rstudio that should be checked on.
Closed Blosberg closed 6 years ago
Blosberg
commented
6 years ago The problem was a parsing error in Rstudios read.csv() so the pipeline is fine, but there's something else weird going on in Rstudio that should be checked on.
upon reading the sam file into Rstudio from the output of minimap2 Additional alignment entries have been observed that do not trace back clearly to any particular read from the input data. These tend to have entries such as the following: [1] SA:Z:chr7,128210465,-,261S269M29D640S,1,54; [2] SA:Z:chr1,145969268,+,109S166M1D791S,0,24;
-- These entries have also been filtered out in subsequent steps: current hypothesis is that this is an Rstudio issue, and that this is only cropping up in my debugging. To check for sure, I'll run another scan on the sam file while only printing the first column, and then checking for unique reads.