Dear rwnull,
Thank you for providing this useful tool.
Following the instructions in the README, I was able to successfully create a basic single probe set. However, when I attempted to use the BLASTn option, the tool failed to generate outputs.
Here is the command I used:
python ./HCR.py -blast ./ref.fasta -in ./geneA.fa -amp S41
version of the tools:
blastn 2.16.0+
Python 3.13.5
biopython 1.85
numpy 2.3.0
openpyxl 3.1.5
pandas 2.3.0
And here is the output I received:
Amplifier Chosen: S41
/(path to the file)/ref.fasta is a fasta file.
Transcriptome reference: ref.fasta, located in the directory /(path to the file)
/(path to the file)/geneA.fa is a fasta file.
length of input sequence is 1921
Sorry there were no probes that we could make. Double check your sequence and/or loosen your constraints.
I would appreciate your help in determining whether this is a bug or a configuration issue on my end. If you have any suggestions or insights, I’d be grateful.
Best regards,
ninui23
Dear rwnull,
Thank you for providing this useful tool.
Following the instructions in the README, I was able to successfully create a basic single probe set. However, when I attempted to use the BLASTn option, the tool failed to generate outputs.
Here is the command I used:
python ./HCR.py -blast ./ref.fasta -in ./geneA.fa -amp S41version of the tools:
And here is the output I received:
I would appreciate your help in determining whether this is a bug or a configuration issue on my end. If you have any suggestions or insights, I’d be grateful.
Best regards,
ninui23