I have loaded multiple Illumina fastq files onto a server and I’m utilizing mothur via command line. My end goal is to use the trim.seqs maxhomop command to remove poly-A runs in my data, which has been successful for a number of the files I’ve entered. However for a handful I enter the command:
mothur > fastq.info(fastq=30_1.fastq)
And get the following:
[ERROR]: Blank quality name.
Another error reads:
[ERROR]: Lengths do not match for sequence D8GSQ5P1:2:1102:5739:28694#0/1. Read 101 characters for fasta and 100 characters for quality scores.
I’m not sure what to do about blank quality names, but is there a way to change a parameter to allow for different lengths of characters in the fasta and quality scores?
Additionally, is there a way to set up batch run to run fastq.info from multiple fastq at the same time?
Thanks for your help!
~Erin