search

Isabella136 / AmrPlusPlus_SNP

GNU General Public License v3.0
1 stars 1 forks source link

Standalon running - incomplete results #29

Closed gustavogregoracci closed 11 months ago

gustavogregoracci commented 1 year ago

Dear Natalie, Sorry to bother you again. Your new congif.ini file solved our run issues and we've been able to apply it to our samples. We have hundreds of alignment matches against Megares in sam files, dozens of which require SNP confirmation. But when we run your script, our results file come back with ~15 evaluations only. I suppose the genes that do not require SNP confirmation would be ignored, but I was expecting that all which require SNP confirmation would be evaluated. Any thoughts on why not? Any files we could share to improve understanding? Thanks for you time!

Isabella136 commented 1 year ago

Can you share an example of a sam file and its results?

gustavogregoracci commented 11 months ago

Many apologies for thte delay. End of semester hit hard. :) Please, try to see the files in this link: https://drive.google.com/drive/folders/1dbXyFeR2b4Z2GUuuYlmW515jHm8iezv-?usp=sharing

Isabella136 commented 11 months ago

I don't have access to the files; do you want me to send a request for access through Google Drive?

gustavogregoracci commented 11 months ago

Please

Isabella136 commented 11 months ago

I'm confused; what is the problem exactly?

gustavogregoracci commented 11 months ago

So, our alignment against Megares provided thousands of hits. Disregarding the ones that did not require SNP confirmation, shouldn't all other be tested? It would still be up to hundreds or perhaps thousands, but we get only 15 results back. Could you try to explain to me?

Isabella136 commented 11 months ago

All of them are tested, but most of the alignments didn't contain any of the key nucleotides or amino acids required for resistance, so they come back as susceptible

gustavogregoracci commented 11 months ago

But the totals don't seem to match. Shouldn't they? It seems AMR++_SNP returns way fewer sequences...

gustavogregoracci commented 11 months ago

Or perhaps they do. The normal genes are indeed abundant.

Isabella136 commented 11 months ago

They should only return alignments that have been confirmed as resistant. To explain it a bit more clearly, lets take a random reference, gene A, which has been aligned to 200 query sequence in a sample: