spacepharer

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Too many FASTA files with spacers

2

Hi, I'm encountering an issue while attempting to run the command: `spacepharer easy-predict spacers/*.fna targetSetDB predictions.tsv temp/` I have approximately 35,000 FASTA files containing spacers, each corresponding to a different...

aziele

Example with CRISPR output files (piler-cr and CRISPRDetect) produces empty file

2

Dear authors/developers, Please find the relevant information for my issue below. Please do not hesitate to ask for more informaiton. Looking forward to hearing from you. ## Expected Behavior Non-empty...

shaman-narayanasamy

Input and output files

1

I want to predict the phage-host using the SPacePHARER a tool developed by your team. I have metatranscriptome data and want to screen the bacteriophages. My question is what will...

pankaj209h

Right now we extract potential PAMs based on regular expressions. We don't have any measure to quantify how confident we are in the PAM prediction. Additionally a high confidence PAM...

milot-mirdita

Query database size and predictmatch matches

1

Hello, I am using SpacePHARER for a project, and had a few questions about how query database size can affect predictmatch results. I ran spacepharer predictmatch for two query databases,...

imrambo

Dear authors/developers, It is me again! (Sorry) I am attempting to run `predictmatch` on a set of spacers against a virome database. Briefly, the spacers were extracted directly from metagenomics...

shaman-narayanasamy

Dear authors/developers, Thanks for maintaining `spacepharer`. I was attempting to created/overwrite a query database of spacer sequences. Despite `createsetdb` clearly warning that the database will be overwritten in the stdout,...

shaman-narayanasamy