Trobleshooting import reads

[jwdebelius (Justine Debelius)]

Hi @mstagliamonte,

Have you tried the manifest format? It requires a bit more work up front from you for importing, but I think it will make your life easier over all.

There's some development for automatic manifests in both R and python which might be of interest.

Automatic Manifest Maker in Python3

Hello all! Since joining this community my coding skill has improved quite a lot. When I first started I made this tutorial here, which is functional, but not ideal. I decided to update it to be a bit more useful for people here using Python 3. Hope it helps you all. https://github.com/Micro-Biology/BasicBashCode/blob/master/BasicScripts/Q2_manifest_maker.py Hosted on github so I can edit it, feel free to use however you want, if you add other formats please share below. Any feedback please …

Automatic Manifest Maker in R

Here I present my tutorial for making a 'Manifest.csv' automatically using an R conda environment, to be used to import data according to the " “Fastq manifest” formats" part of the Importing data tutorial. I wrote this script because we intended on running a lot of analyses through QIIME2 and I did not want ot manually make a manifest file to import it every time. This guide assumes you have a version of conda installed, and that files at names samplename.R1.fastq.gz for forward reads and sam…

Best,
Justine