cutadapt outside of QIIME2

Other Bioinformatics Tools
1
  • I am using cutadapt outside of QIIME2, actually in a python script with a subprocess call
  • Data I have is in fastq format and each sample file that I have, there are several rows and each row - the sequences are like in the range of 10000 plus in length
  • Issue I am having is, if I keep -a as auto i.e. 'A' and min_length say set to 1000, I get empty preprocessed output file
  • I realized the mistake and reduced min_length to 80 and quality_trim_len as 3, I get almost same size output file as the input file, so doesn't trim much at all.

Please advise what I should be doing, here's my sample cutadapt command
cutadapt --cut 2 -m 80 -q 3 --report minimal r"...inputpath\file1.fastq" -o ./prepped_temp/train_files\ca_file1.fastq

2

Hello @pankaja12,

Have you tried to import your data into qiime2 and use the cutadapt plugin? We will be better able to help troubleshoot if you do, for example so we can look at the demux summary visualization which gives lots of helpful information about raw demultiplexed sequences.