trim seqs

I have MiSeq data that was successfully grouped with the make.contigs file. However, I want to use trim.seqs to get rid of the primers, but it keeps putting most of the sequences in the scrap file. I know this is because the primers are not at the start of the sequence. Is there a way I can use trim sequences to search for the primer and get rid of all the sequences prior to that? Or, do I have to put in all the barcode information (I used the double barcodes as in the MiSeq paper by Kozich et al, 2013). If so, what is the best way of doing that that includes the barcodes, spacer and primers? It is not specifically listed in the trim.seqs command information. Thanks!

If you followed the approach we used in Kozich, there won’t be any barcodes or primers on the sequences and so trim.seqs won’t be necessary. If you aren’t following the MiSeq wet lab SOP that we posted, can you give some more details of what you’ve done?

I emailed you back in November and ended up getting instructions from Jim Kosich about setting up a sample sheet. However, the sequencing provider could not make the sample sheet work last time (miseq rejected it) so they demultiplexed the run afterward. So, the sequences were already split into samples when I got the data, and I then created a stability file based on the names. They have the barcode, linker and primers still in the sequences. I would like to remove them so I can work with a smaller number of sequences- right now it is at 3.5 million, with only 22 samples (out of 96). Any suggestions would be appreciated.

Could you post a sample sequence with the barcode, linker and primer?

I’m also curious about this. I am following the Miseq tutorial and I am not sure what primers were used, if there are any adapters/barcodes/linkers on the sequences, and if the make.configs command does this automatically. I also cannot find the paper that was mentioned as being published in AEM. I’d like to use the tutorial to test the abilities of a cloud based tool called CloVR. It would be really nice if I could get the results for the sample test or the entire test. Please help!