Hello everyone, I am Fernando.
Recently I started a de-multiplex task and I’m facing a trouble related to metadata in .tsv format.
I’m doing a paired end de-multiplexing. I’m trying the cutadapt tutorial which refers a .tsv metadata and also a barcode reference file in categorical column format.
when I try to run the de-multiplexing, this is the message in my terminal: Invalid value for “–m-forward-barcodes-file”: There was an issue with
retrieving column ‘Barcode’ from the metadata:
I’ve already verified .tsv metadata on keemei, and I did not get any notifications of any format error.
My bardcoe file consists of only one column with “featureid” as header.
I assume, for some reason, there is no compatibility between my barcode reference and my .tsv table, but I haven’t found any barcode file example to compare with.
Can anyone please help with this, I’m totally stucked.
I think you need at least two columns: one is your feature-id column (the name) and the second is the barcode (I think you’d call it barcode here). So, if you only have one column (featureid), you don’t have a column (Barcode) to retrieve. (Although if you’re re-doing your metadata, I’d actually recommend naming the first column sample-id or something similar because you’re splitting data into samples, not features.)
well, I followed your advice adding the “sampleid” column to my barcode file and making headers to match between metadata file and barcode file, but it didn’t work out either.
I also try with a .txt format for metadata file and it gave the same result. The good thing (I think) is I get the same message every time, so the problem must be focalized, and there is a value of the barcode column in the metadata file which is corrupted. I think I will create again the table, as you mentioned, in order to check and avoid any error. Let’s see what happens
If you or anybody else have a tip, please share it.
yes @jwdebelius, I do
headers in my metadata file are: sampleid, barcode, flag-name, position & sample-type
while the headers of barcode file are : sampleid, barcode
and this are the first lines of “Barcodef”:
sampleid barcode
Fl1 ACACAGAAGGTC
Fl2 ACAGCAGAGGTC
NOTES:
I was succesfull importing the Raw-paired-end.qza artifact
All slashes are inverted, i wrote them this way because invert slashes weren’t visible when copied (sorry).
Metadata and barcode files for reverse reads have the same format as those shown in this replay
There is no hearts enough to express how I love your last post. Thank you for all your support. That was exactly the problem with my script, I was retrieving something else.
Thank you once again and don’t miss me, II’m sure 'll be back with more issues ja ja ja
It happens to everyone. Im pretty sure “I can’t remember who how i spelled it”/where it is/to activate my environment is a semi-universal error and just means you’re a bioinformatician.
Hopefully, now you know to check your capitalization for next time.
that if you try the lower case column name, it will work.