Hello, I am working my way through an RNA-editing flowthrough and am now trying to clip-off the Illumina 5'-end adapters. I have aligned my paired-end reads with bwa samse -n 4, and next have added headers, sorted and removed duplicates, to find out that I need to remove the Illumina adapter sequences. I am about to use the Picard tool CleanSam.jar to perform a soft-clip of my data and would like to ask the community is such "cleaning" is appropriate for my purposes: again trimming of 5'-end Illumina adapters. Thanks in advance!
I usually remove adapters prior to mapping. I wrote a program called SeqPrep to do this. More reads will map when you trim before mapping, also my program uses the overlap between the pair of reads as well as matches to the adapter (you are doing pairs, right?). That said if you are not doing pairs of reads, do not use SeqPrep, it is only for paired reads. If you are using single ended reads any tool that does adapter trimming (think there is one in GATK as well as Picard's CleanSam). The lab I used to be in used Trimmomatic for adapter trimming. There are a ton of programs though that will work reasonably well on single-ended reads if that is what you have.