Question: pipeline for 16sRNA miseq illumina
1
gravatar for Quak
6.0 years ago by
Quak380
United States
Quak380 wrote:

I have ran mothur and uparse pipeline and they were very straighforward. now I am giving a try to qiime - but it is a headache - so un organized and not similar to what I experienced so far.

for example, I have to make a mapping file; but seems I am not pointig to the fastq file in the mapping file ?!!

In my data the reverse data quality is so bad; so I am going to use only the forward read.

so my question is how to for a mapping for for such a set up and it would be great if someone gives a hint how to "Pick OTUs through OTU table" !

Qiime mapping file example looks like

#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description

I wonder which column is for the path to the fastq files ?

Also, I already have removed barcoes, primers with other tools

 

Thank you

qiime miseq • 4.8k views
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Quak380
3
gravatar for marina.v.yurieva
6.0 years ago by
Farmington, CT
marina.v.yurieva520 wrote:

QIIME is very helpful but can have it's painful moments. Here is the pipeline for the Illumina data: http://qiime.org/tutorials/processing_illumina_data.html 

I make fake mapping file because i already have fastq without any adapters. Just make sure the names are correct but the sequences can be fake. Convert fastq to fasta and use the pipeline.

ADD COMMENTlink written 6.0 years ago by marina.v.yurieva520

I have updated my question to make it more clear;

basically, in the mapping file which column corresponds to the path to fasta files ? Thanks

ADD REPLYlink written 6.0 years ago by Quak380
1

#SampleID column

ADD REPLYlink written 6.0 years ago by marina.v.yurieva520
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