I have been trying to trim my fastq files, and I am running into problems. I used the "Trim leading or trailing characters" tool to trim the first 10bps of my reads (from 51bp -> 41bp for each read) with the following conditions:
this dataset LV_12_S24_L005_R1_001.fastq Trim this column only 0 Trim from the beginning up to this position 11 Remove everything from this position to the end 50 Is input dataset in fastq format? Yes Ignore lines beginning with these characters
After I run this, I get an error message saying:
Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/galaxy/tools/filters/trimmer.py", line 111, in <module> main() File "/cvmfs/main.galaxyproject.org/galaxy/tools/filters/trimmer.py", line 75, in main invalid_starts[i] = chr( int( item ) ) ValueError: invalid literal for int() with base 10: '-q'
I have previously used the same tool to trim sequences for my previous experiments, and had no problem. Strangely, when I try to repeat exactly the same trimming process using the same parameters and same fastq file, I cannot get the trim to work.
Any help would be appreciated,