Hi,
I have been using PPQT for .bam files to obtain the fragmentsize of the reads.
It usually works fine, however, for some files I get the following error:
Error in pdf(file = iparams$output.plot.file, width = 5, height = 5) :
cannot open file 'file.sorted.pdf'
Execution halted
When this happens I still get an output file, however, col3 contains only 1
value instead of the usual 3.
This is my input:
Rscript run_spp.R -c=file.sorted.bam -savp -out=file_PPQT.csv
The files that give this error are usually mapped with bwa (and contain
duplicate reads and reads mapping to repeat regions), while files that do not
produce this error are mapped with ELAND (and contain duplicate reads but not
read mapping to repeat regions).
How can I fix this error, and can I trust the output data?
Thank you for your help,
Saartje (Nijmegen, The Netherlands)
Original issue reported on code.google.com by Saartje....@gmail.com on 15 Mar 2013 at 8:09
Original issue reported on code.google.com by
Saartje....@gmail.com
on 15 Mar 2013 at 8:09