search

andersen-lab / ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
https://andersen-lab.github.io/ivar/html/
GNU General Public License v3.0
115 stars 39 forks source link

Ivar-Freyja Pipeline creates +/- bases and "#Name?" cells #142

Closed EESI-jv545 closed 1 year ago

EESI-jv545 commented 1 year ago

Describe the bug Hi everyone, I'm currently using an Ivar-Freyja pipeline that processes a set of 414 COVID-19 samples, and I am able to get output TSV files that give positions on the single nucleotide variants. I noticed how the TSV files have positions with alternate base like -T or +C, but when I downloaded these as CSV files, their cells would only give errors saying "#NAME?". If someone could tell me why are there +/- bases, as well as how I can fix the #NAME? issue, that would be great!

The code and files should be attached too; I couldn't get the TSV file uploaded since Github doesn't support that format, but I pasted a screenshot of the file with some of the positions listed

Expected behavior There are supposed to be only letter characters in the ALT columns; these characters are nucleotide bases (A,T,C,G). Instead, the TSV files have sections with characters like -T, and the CSV files have #NAME? in those spots

Screenshots

CDM6_S3_variants.csv image image image

EESI-jv545 commented 1 year ago

Solved in here: https://github.com/andersen-lab/Freyja/issues/96