Rebuilding TE landscape
Chloisf opened this issue · 1 comments
Hello!!
Thank you for dnaPipeTE I am finding it very straightforward to use !
However I have a small question. I am trying to rebuild the landscape plots on my R console so that I can display them at once for several species I analyzed.
So I found the landscapes.R script as well as the factors_and_colors and reads_landscapes tables which are necessary.
However, in the R script, it seems that a table "ttl" is also necessary to rebuild the plot. I am having trouble understanding what this table is. Where can find it in the dnaPipeTE output ?
Thank you !
Hello and thank you for your kind words!
The file you are looking for is blast_reads.counts and can be found in the output folder. This is the total number of reads used for quantification.
Rscript landscapes.R reads_landscape factors_and_colors blast_reads.counts
It will automatically create a new file with the landscape graph.
Cheers,
Clément