Dear Qiimer, I know it is common that illumina 16S sequencing does not include primer sequence but it will be nice to have this option to enable it? It is not convenient to using the parameters in split_libraries_fastQ.py on split_libraries.py after converting it to fastq and qual file.
For most of the cases, the primer sequences are not part of the sequence (like barcode+sequences), but for in-line barcoding, the primer are part of the sequences, just like 454 (like barcode+primer+sequence). We would need to trim off this sequences in the latter case. This option for trimming primer is available in split_libraries.py previously but not part of the one for fastq file.
The following the request from Mike:
Hello all,
I'd like to add to this request myself. I will be receiving data back from a collaborating sequencing facility which will contain both the forward and reverse primers within our illumina reads. I think they do this for quality control purposes. So, I'd like to see a way to remove / trim the forward primers from the fastq data within split_libraries_fastq.py or at least down stream with one of the other scripts. Maybe update the 'truncate_reverse_primer.py' script to 'truncate_forward_and_reverse_primers.py' that can be used on the output of split_libraries_fastq.py?
gregcaporaso
commented
11 years ago
Dear Qiimer, I know it is common that illumina 16S sequencing does not include primer sequence but it will be nice to have this option to enable it? It is not convenient to using the parameters in split_libraries_fastQ.py on split_libraries.py after converting it to fastq and qual file.
For most of the cases, the primer sequences are not part of the sequence (like barcode+sequences), but for in-line barcoding, the primer are part of the sequences, just like 454 (like barcode+primer+sequence). We would need to trim off this sequences in the latter case. This option for trimming primer is available in split_libraries.py previously but not part of the one for fastq file.
The following the request from Mike:
Hello all,
I'd like to add to this request myself. I will be receiving data back from a collaborating sequencing facility which will contain both the forward and reverse primers within our illumina reads. I think they do this for quality control purposes. So, I'd like to see a way to remove / trim the forward primers from the fastq data within split_libraries_fastq.py or at least down stream with one of the other scripts. Maybe update the 'truncate_reverse_primer.py' script to 'truncate_forward_and_reverse_primers.py' that can be used on the output of split_libraries_fastq.py?
-Thanks! -Mike