Now I am working on the Iso_seq Analysis using the Tofu program, I am intended to intergrated all the analysis (including classify,cluster,Removing Redundant Transcripts Analysis,find fusion) in a perl script. But I run into an error when I run the Tofu program by using the following perl script :
`/share/biosoft/smrtanalysis/current/smrtcmds/bin/smrtshell && source /share/software/python_virtualenv/bin/activate && collapse_isoforms_by_sam.py --input $fafile -s $fafile.sorted.sam -o $fafile.sorted.5merge>$fafile.sorted.5merge.log`;.
The program only go into the smrtshell and doesn't run the following script. What is the matter?
Is there any advice to intergrated the Iso_seq Analysis workflow and the TOFU workflow into a perl script?
Thanks a lot!
`/share/biosoft/smrtanalysis/current/smrtcmds/bin/smrtshell && source /share/software/python_virtualenv/bin/activate && collapse_isoforms_by_sam.py --input $fafile -s $fafile.sorted.sam -o $fafile.sorted.5merge>$fafile.sorted.5merge.log`;.
The program only go into the smrtshell and doesn't run the following script. What is the matter?
Is there any advice to intergrated the Iso_seq Analysis workflow and the TOFU workflow into a perl script?
Thanks a lot!
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