QIIME mapping file: understanding: linker primer seq column

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Sanjeev Sariya

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Mar 9, 2016, 11:22:22 AM3/9/16
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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:

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

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
qiime_map.txt

Embriette

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Mar 9, 2016, 11:54:42 AM3/9/16
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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

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Mar 9, 2016, 12:12:36 PM3/9/16
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Hi Embriette,

Thank you for the lightening fast reply. :)
Thanks much for confirming with dummy sequence.!

Best,
Sanjeev
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