importing demultiplexed pair end data

hello, I have obtained demultiplexed paired end data and have a metadata file. I took the barcodes obtained from the forward and reversed read and created one single file (manifest.tsv) file in excel. I also have unzipped all my forward and reverse end data into a folder. However, each time I try to import it the process shows error.I have obtained these file so far . One zipped file with forward and reverse read for all samples, one tsv(metadata file), one unzipped file ( fastQ file with forward and reverse read), one tsv file (generated in excel) which has the sample id and absolute path for all the forward and reverse read,. I want to do OTU and ASV analysis.I have already tried reading all the forum answers and documentation on the website but am still confused. Specially because I download the data manually from my email and they use wget.


It is hard to tell without seeing the actual error message you are receiving, but I think you are on the correct path by making a manifest file. While unzipping the individual files and then zipping them together does seem like the thing to do, this is not exactly what import is expecting. Generally, a standard practice is to place all of your compressed files in a directory together, then create your manifest so that you point to each of those files directly in that directory. Then when you are running your import command, you point --input-path to that directory, as you can see in the manifest section of the importing tutorial. If you are going to run the import the command from the parent directory of your data directory, you can use the environment variable $PWD in your manifest to represent that location if you do not want to specify the full path. If you run into any other issues, could you post a screenshot of the error you are getting and possibly a copy of the log file? This makes it much easier to help :slightly_smiling_face:

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.