h836472
commented
2 months ago Dear Sandro,
To some extent, the function you describe is already available in ContScout. With the -G / --genome_filter switch, contigs that are tagged at the consensus call step as contaminationare removed from the DNA fasta and corresponding annotation GxF files. At the same time, currently, there is no option for the selective masking of individual "alien-looking" genes within those contigs that are labeled as non_contaminant at the consensus call stage.
Hope this explanation helps,
Balazs
On Thu, 1 Aug 2024 at 09:37, Sandro Valenzuela @.***> wrote:
Dear Balazs, I was wondering if it is possible to remove the contaminated genes/proteins from the original contigs. I have the filtered outputs which are the proteins. However, it would be useful to have the decontaminated scaffolds as well for further analyses. Is there a way to propagate the filters to the original contigs? I was thinking in hardcoding the .gff and the original .fna to break down the contigs. Is there an option for that or the output of the pipeline is until the filtered proteins?
Thank you very much in advance, Sandro
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Dear Balazs, I was wondering if it is possible to remove the contaminated genes/proteins from the original contigs. I have the filtered outputs which are the proteins. However, it would be useful to have the decontaminated scaffolds as well for further analyses. Is there a way to propagate the filters to the original contigs? I was thinking in hardcoding the .gff and the original .fna to break down the contigs. Is there an option for that or the output of the pipeline is until the filtered proteins?
Thank you very much in advance, Sandro