I'm using QIIME 1.9.1, on linux. I've Illumina dual index, V3-V4, 301 BP data. I've forward, and reverse primer. Data generated by 2-step PCR sequencing.
I do not have LinkerPrimerSequence information available with me.
I can get my data through split library fastq after couple of hacks.
I'm confused with mapping file.
If I look at URL:
It doesn't have forward, and reverse primer column in it.
2) I read URL:
It says: "As a consequence, the LinkerPrimerSequence in the mapping file is not important. "
However if I leave LinkerPrimerColumn blank in mapping file, validation report shows that column in Red.
To circumvent that I used dummy string: AAAAAA
I dug in forum, and found/read that split library fastq shan't trim/remove primers from my demultiplexed reads. For that I'm to use script to get rid of them.
1) After providing dummy LinkerPrimerSequence are there any ill-effects?
2) If I go as per URL in point 2, LinkerPrimerSequence should not be necessary but I get red columns after validation, why?
3) How do I fix empty LinkerPrimerSequence column to avoid red warnings?
Attached mapping file that worked.
Hope I can have some more understanding with mapping file that would help me smoothen my work.