QIIME mapping file: understanding: linker primer seq column

[Sanjeev Sariya]

Hi There,

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. 

1)

If I look at URL:

http://qiime.org/_static/Examples/File_Formats/Example_Mapping_File.txt

It doesn't have forward, and reverse primer column in it.

2) I read URL:

http://qiime.org/1.2.1/tutorials/processing_illumina_data.html

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

3) 

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.

Questions:

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.

Thanks,

Sanjeev

[Embriette]

Hi Sanjeev,

You are right-for split_libraries_fastq.py, the Linker primer seq is not needed. However, QIIME still requires that column in the mapping file as it is required for split_libraries.py. This is legacy; with QIIME 2.0, the columns will be revisited.

You can go ahead with the dummy sequence you provided.

Thanks!

Embriette

[Sanjeev Sariya]

Hi Embriette,

Thank you for the lightening fast reply. :)

Thanks much for confirming with dummy sequence.!

Best,

Sanjeev