Does anyone know how to edit reads after alignment has been done using gsAmplicon software? I want to go back and edit any variants that I know are sequencing errors.
-
-
I just found that there is no function to edit reads on the 454 software. Does anyone know a program that would allow me to edit reads post alignment. I dont want filter out the reads completely, I want to be able to edit the errors and use them for alignment and analysis. -
Well if that really is what you want you could go from sff to fasta, alter the fasta and go back to sff. You can use the sfftools/sffinfo provided by Roche.Comment
-
I thought sfftools was only provided with the 454 machine which I dont have. I had my samples sequenced at a core bioinformatics lab.Comment
-
From what I understand they'll give you the programs you need if you ask nicely:
I think there also are some open source variants of the tools but I never used them.Comment
-
I will look into that.
thank you for your help!Comment
-
You can't go back from FASTA/Q and re-create SFF. In theory you could but nobody wrote such code yet. As far as I am aware of the status in biopython, Roche sfftools, flower.Originally posted by Zaag View PostComment
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...Today, 06:46 AM -
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment