Greetings!
Since out experiment contains 100+ libraries, the gene body coverage line plot and heatmap plot are unable to display all the names. We've also run gene body coverage on the individual input BAM files.
We realize that it is possible to take the *.txt output from individual input runs and convert them to line plots and heatmaps, but since we are new to R, we had to put in some time to get that done. So as undergrad newbies to R, and NGS, may we request some additional feaures to your RSeQC as optional flags while runnin geneBodyCoverage:)
A. suppress the input names altogether
B. shorten names to contain just the unique part of it as the basename
B. change margins
C. in line plot only mention names of inputs with the x% most deviation from the rest (x = user defined)
D. ensure plotting and legend listing are based on natural rather than the default alphabetical sort
Thanks, in advance.
Lotte
Greetings!
Since out experiment contains 100+ libraries, the gene body coverage line plot and heatmap plot are unable to display all the names. We've also run gene body coverage on the individual input BAM files.
We realize that it is possible to take the *.txt output from individual input runs and convert them to line plots and heatmaps, but since we are new to R, we had to put in some time to get that done. So as undergrad newbies to R, and NGS, may we request some additional feaures to your RSeQC as optional flags while runnin geneBodyCoverage:)
A. suppress the input names altogether
B. shorten names to contain just the unique part of it as the basename
B. change margins
C. in line plot only mention names of inputs with the x% most deviation from the rest (x = user defined)
D. ensure plotting and legend listing are based on natural rather than the default alphabetical sort
Thanks, in advance.
Lotte