Hi, my quality socre plots are:
But I lost the information of primers / barcodes for these paired sequencing.
So I don't know how to do trim procedure.
I have some questions and need for helps:
Thanks in advance!
Hi @KE_XU,
The best way to do this is to contact the person who sequenced/processed the data, because you’ll probably want to include it in your manuscript! If it’s published, check the paper. If its your data, ask your sequencing center. (And in general, make friends with the people who sequence your data. They know all kinds of things that we can’t predict).
You could try it and see. It seems reasonable.
Best,
Justine
@jwdebelius is 100% on finding out the answer from the person who sequenced/processed the data! If for some reason you can’t, you could look at the first ~20bp on both sides and compare it against the common primer sets. Example 515F GTGCCAGCMGCCGCGGTAA and 806R GGACTACNVGGGTWTCTAAT. Here is a list of common primers you could look at:
| Primer name | Marker gene | Target region | Sequence |
|---|---|---|---|
| V1_27F | 16S rRNA | V1-V3 | AGAGTTTGATCMTGGCTCAG |
| V3_534R | 16S rRNA | V1-V3 | ATTACCGCGGCTGCTGG |
| V3_357F | 16S rRNA | V3-V4, V3-V5 | CCTACGGGAGGCAGCAG |
| V4_515F | 16S rRNA | V4, V4-V6 | GTGCCAGCMGCCGCGGTAA |
| V4_806R | 16S rRNA | V3-V4, V4 | GGACTACHVGGGTWTCTAAT |
| V5F | 16S rRNA | V5-V6 | RGGATTAGATACCC |
| V5_926R | 16S rRNA | V3-V5 | CCGTCAATTCMTTTRAGT |
| V6R | 16S rRNA | V5-V6, V4-V6 | CGACRRCCATGCANCACCT |
| 18S_V9_1391_F | 18S rRNA | V9 | GTACACACCGCCCGTC |
| 18S_V9_EukBr_R | 18S rRNA | V9 | TGATCCTTCTGCAGGTTCACCTAC |
| ITS1F | ITS | ITS1 | CTTGGTCATTTAGAGGAAG*TAA |
| ITS2 | ITS | ITS1 | GCTGCGTTCTTCATCGA*TGC |
| 5.8SR | ITS | ITS2 | TCGATGAAGAACGCAGCG |
| ITS4 | ITS | ITS2 | TCCTCCGCTTATTGATATGC |
Thanks for your help and provides this reference!
I have another question about checking the sequencing.
How could I generate the sequencing output from demux.qza?
Thanks in advance.
