Hello,
I have run the PhageTerm.py script and am getting an empty re-ordered .fasta file. I am unsure of how to troubleshoot this issue.
My phageterm pdf file indicates that there are multiple preferential termini on the forward strand and one obvious termini on the reverse strand. My thought is that the presence of multiple termini make it hard for the program to choose one by which to re-order. If this is the case, is there a way by which I can have the program do this?
My line of code is:
ptv-py3_release_1/PhageTerm.py -f LayLake_S8_L001_R1_001.fastq -p LayLake_S8_L001_R2_001.fastq -r pilon_laylake.fasta --report_title putative_phage
The output .fasta file is empty.
Any suggestions would be appreciated!
Melissa
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It is hard for me to give a decisive answer on this case, but yes, PhageTerm is usually conservative and will not suggest the re-organization it there is an uncertainty with multiple termini. I would have to look at the report to have a better idea of what is happening there... If you want to send me your report I can have a look:
julian.garneau@unil.ch
Cheers,
Julian
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
I have run the PhageTerm.py script and am getting an empty re-ordered .fasta file. I am unsure of how to troubleshoot this issue.
My phageterm pdf file indicates that there are multiple preferential termini on the forward strand and one obvious termini on the reverse strand. My thought is that the presence of multiple termini make it hard for the program to choose one by which to re-order. If this is the case, is there a way by which I can have the program do this?
My line of code is:
ptv-py3_release_1/PhageTerm.py -f LayLake_S8_L001_R1_001.fastq -p LayLake_S8_L001_R2_001.fastq -r pilon_laylake.fasta --report_title putative_phage
The output .fasta file is empty.
Any suggestions would be appreciated!
Melissa
Hi Melissa,
thanks for your message,
It is hard for me to give a decisive answer on this case, but yes, PhageTerm is usually conservative and will not suggest the re-organization it there is an uncertainty with multiple termini. I would have to look at the report to have a better idea of what is happening there... If you want to send me your report I can have a look:
julian.garneau@unil.ch
Cheers,
Julian
Julian,
I will send you a copy straight away. Your help is truly appreciated.