BioScope Mapping Multiple csfasta-Files

[DNAjunk]

Hello

Does anybody know how it is possible to map reads from several csfasta files (e.g. different samples on different panels) with the BioScope Mapping Pipeline without running the program several times?
The variable "mapping.tagfiles.dir" in the map.ini file is set to the directory where all the csfasta files are located. When I put several files there, BioScope maps the reads from only one of these files.

Many thanks!

[westerman]

No easy way that I know. I usually combined the files together while renaming the reads so that (1) there are no naming conflicts and (2) the reads are named 'in order' (which at least the older versions of Bioscope were sensitive to).

Let me know if you want my rather primitive perl-based renumbering script. Good only for fragment projects.

[DNAjunk]

Yes, I am interested in the renumbering script. I certainly could use it when I have samples with low number of reads. Thanks in advance!

[clariet]

I did it once for a few bacterial samples. I just put multiple .plan file (each plan file has one ini file) in one shell script. It did the job.

[westerman]

I did it once for a few bacterial samples. I just put multiple .plan file (each plan file has one ini file) in one shell script. It did the job.

Did this merge all of the reads into one large mapping? (which is what I believe the original poster wanted and what my renumbering script will accomplish) Or did you run multiple instances of Bioscope and thus create multiple mappings via your shell script?

[DNAjunk]

PS: Yes, I want that BioScope puts all read together somehow, and runs the script and reads the reference genome into memory only once and not for each reads file separately.