Question: Removing Barcodes with UPARSE/USEARCH
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gravatar for gaiusjaugustus
4.2 years ago by
United States
gaiusjaugustus150 wrote:

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?

 

 

uparse microbiome • 1.3k views
ADD COMMENTlink modified 15 months ago by 4971574050 • written 4.2 years ago by gaiusjaugustus150
1
gravatar for gaiusjaugustus
4.2 years ago by
United States
gaiusjaugustus150 wrote:

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.

ADD COMMENTlink written 4.2 years ago by gaiusjaugustus150
0
gravatar for 497157405
15 months ago by
4971574050
4971574050 wrote:

I have encountered the same problem now. How did you solve it ? I was inputting a FASTQ file, but it still shows an error

ADD COMMENTlink written 15 months ago by 4971574050
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