Removing Barcodes with UPARSE/USEARCH

Question

[gaiusjaugustus]

I'm working on pre-processing my microbiome data with UPARSE/USEARCH (http://www.drive5.com/). I need to remove my barcode reads. There is a script available for this: http://drive5.com/python/fastq_strip_barcode_relabel_py.html

I am getting the following error:

File "USEARCH_py/fastq_strip_barcode_relabel.py", line65, in <module> fastq.ReadRecs(FileName, OnRec)
File "/home/qiime/Documents/USEARCH_py/fastq.py", line 140, in ReadRecs ReadSeqs(FileName, OnRec)
File "/home/qiime/Documents/USEARCH_py/fastq.py", line 127, in ReadRecs assert Line[0] == '@'
AssertionError

Can anyone help me identify the problem?

[497157405]

I have encountered the same problem now. How did you solve it?

I was inputting a FASTQ file, but it still shows an error

Answer 1

[gaiusjaugustus]

assert Line[0] == '@' means that the line should start with a @. In this case, it's checking that it is a FASTQ file. I was inputting a FASTA file from the previous step, which uses > as a line delimiter.