Trimming the primers from paired end reads

[Razi]

Hi every one

I received some paired end reads containing specific Lexogen primers. So before assembly the primers must be removed from the reads. According to Lexogen protocol I must remove 9 nucleotides from 5' side of R1 and 6 nucleotides from 3' side of of R2. Is there any especial command in BBMap or any other software to accomplish this kind of trimming? In BBMap I just found command for removal specific number of nucleotides from tail of a read but for 5' side of the read I could not find a command as well. Would you please guide me to trim my reads?

[GenoMax]

This question is cross-posted and has been answered: https://www.biostars.org/p/282328/#286154

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I suggest fastp to do automatic adapter trimming, read filtering and quality control. fastp is ultra-fast since it's developed in C++ and with multi-threading support.

fastp has following features:
1, filter out bad reads (too low quality, too short, or too many N...)
2, cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).
3, trim all reads in front and tail
4, cut adapters. Adapter sequences can be automatically detected,which means you don't have to input the adapter sequences to trim them.
5, correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality
6, preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name.
7, report JSON format result for further interpreting.
8, visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).
9, split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.
10, support long reads (data from PacBio / Nanopore devices).

fastp creates reports in both HTML and JSON format.

HTML report: http://opengene.org/fastp/fastp.html
JSON report: http://opengene.org/fastp/fastp.json

fastp is an open source project at github: https://github.com/OpenGene/fastp