search

nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
0 stars 2 forks source link

increasing trim to 19bp #53

Closed crosenth closed 1 year ago

crosenth commented 2 years ago

Increased the primer trimming to match the 19bp right primer CTCCTA... see example below

                                 10        20        30        40
sv-18:                   AGATTGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAGC
                         ::::::::::::::::::::::::::::::::::::::::::
KF5576 AGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAGC
               10        20        30        40        50        60

             50        60        70        80        90       100
sv-18: GGTAGCACAAGAGAGCTTGCTCTCTGGGTGACGAGCGGCGGACGGGTGAGTAATGTCTGG
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
KF5576 GGTAGCACAAGAGAGCTTGCTCTCTGGGTGACGAGCGGCGGACGGGTGAGTAATGTCTGG
               70        80        90       100       110       120

            110       120       130       140       150       160
sv-18: GAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCG
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
KF5576 GAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCG
              130       140       150       160       170       180

            170       180       190       200       210       220
sv-18: CAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAG
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
KF5576 CAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAG
              190       200       210       220       230       240

            230       240       250       260       270       280
sv-18: CTAGTAGGTGGGGTAATGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGAC
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
KF5576 CTAGTAGGTGGGGTAATGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGAC
              250       260       270       280       290       300

            290       300       310
sv-18: CAGCCACACTGGAACTGAGACACGGTCCAGA
       :::::::::::::::::::::::::::::::
KF5576 CAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATAT
              310       320       330       340       350       360
crosenth commented 2 years ago

Steve shared with me the exact primers

crosenth commented 2 years ago

I set the trimRight back to 15, I think we did look at a quality picture on that

nhoffman commented 1 year ago

Looks good to me. Merging.