lucapinello
commented
7 years ago Hi Alex,
To detect the adapter used I suggest you to either blast those sequences or use FASTQC from here: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
In particular you need to use those two modules: 1) http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/10%20Adapter%20Content.html
After you recover the adapter sequence you can read more about the format of the required file here: http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
About your last question, assuming that you have the file CUSTOM_ADAPTER.fa in the correct format you need to add the option like this:
--trim_sequences --trimmomatic_options_string " ILLUMINACLIP:/Users/data/CUSTOM_ADAPTER.fa:0:90:10:0:true MINLEN:40 "
You need to adjust the parameters according to your particular case, please read carefully the trimmomatic manual.
You can also trim the sequences outside CRISPResso with trimmomatic so you don't need to re-run the entire procedure every time.
Regards,
Luca
Hello, I have a bunch a fastq.gz files to analyze, paired end reads. However the adapter sequences are not Nextera and I don't know which ones they are exactly.
Just from looking at the fastq.gz files, can I know which adapter sequences were used, and if so, how can I then trim them with --trimmomatic_options_string ??
I guess I have to create a .fa file similar to the "NexteraPe-PE.fa" file, however I'm not sure how to correctly do this.
I attach the two files (pair ends) of one sequencing. Would you please help me out and guide me as to be able to this by myself in the future? Thank you so much, I would really appreciate it! You tool is very useful and a great contribution to the scientific community. Best, Alex Won_Tae_1_S48_L001_R1_001.fastq.gz Won_Tae_1_S48_L001_R2_001.fastq.gz