Recently I started using PhageTerm on my phage genomes, altough only after some time I noticed that the size of the new contig (83866) created was subtabtially smaller than the inputed contig (105369)
Why the software decreased the size of my contig? How can this be fixed?
Thank you in advance
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Can you help me by telling me what is the result you obtained on that contig after the PhageTerm analysis? That should help me help you.
Only thing I can guess for now, is that your result is possibly a "DTR-long" , and that the repeat region was taken out of the reorganised genome. However, since there is a 21 503 difference between both contigs, that seems pretty big for a DTR, which I think at maximum have been seen at around 10 000 bp. But that is not impossible.
Anyway, I will wait for you, if you can give me a maximum detail about your phage analysis and detail about the phage too if you have some.
Cheers
Julian
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I've attached some of the output files generated by PhagTerm on my latest run.
I used RAST on both assemblies, the bigger one contained new and different CDSs when compared to the smaller sequence generated by PhageTerm. One of the main differences was the RNA content, which the smaller sequence seemed to have none, according to RAST. Also the bigger sequence contained three CDSs identified on the Ribonucleotide reduction subsystem that were'nt present on the PhageTerm output.
It seems that the discarted region contained unique CDSs that weren't present on the PhageTerm output fasta.
Hello there
Recently I started using PhageTerm on my phage genomes, altough only after some time I noticed that the size of the new contig (83866) created was subtabtially smaller than the inputed contig (105369)
Why the software decreased the size of my contig? How can this be fixed?
Thank you in advance
Hi again Gustavo,
Can you help me by telling me what is the result you obtained on that contig after the PhageTerm analysis? That should help me help you.
Only thing I can guess for now, is that your result is possibly a "DTR-long" , and that the repeat region was taken out of the reorganised genome. However, since there is a 21 503 difference between both contigs, that seems pretty big for a DTR, which I think at maximum have been seen at around 10 000 bp. But that is not impossible.
Anyway, I will wait for you, if you can give me a maximum detail about your phage analysis and detail about the phage too if you have some.
Cheers
Julian
Hello Julian,
I've attached some of the output files generated by PhagTerm on my latest run.
I used RAST on both assemblies, the bigger one contained new and different CDSs when compared to the smaller sequence generated by PhageTerm. One of the main differences was the RNA content, which the smaller sequence seemed to have none, according to RAST. Also the bigger sequence contained three CDSs identified on the Ribonucleotide reduction subsystem that were'nt present on the PhageTerm output.
It seems that the discarted region contained unique CDSs that weren't present on the PhageTerm output fasta.
If you need more details I'm available all week
Thank you for the attention
Cheers
Gustavo
Hi Gustavo, thanks for the details,
I forgot to ask you, what procedure did you use to sequence your phage? Did you do illumina TruSeq libraries? Nextera? Other?
For further communications, do you mind writing me on my email ? This will be faster and easier :)
At:
julian.garneau@pasteur.fr