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audy / richardson-2014

Analysis code for the DIPP microbiome study
http://dipp.utu.fi
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Sample Barcode Mapping #34

Closed audy closed 10 years ago

audy commented 10 years ago

Like this

It's probably a good idea to just convert the entire metadata file to this format. Phyloseq (used for importing the data into R) understands this. QIIME is too strict. Going to generate a minimal mapping file instead. Created an to fix this (biocore/qiime #1520)

:frowning: check_id_map.py in QIIME requires barcodes to be unique and we used duplicate barcodes on separate lanes and runs.

Posted a question in the QIIME forum

Example File Format

#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description
#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of
#exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description
#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of
#exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
PC&&&& AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse__I.D._354
PC.355 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse__I.D._355
PC.355 ACAGACCACTCA YATGCTGCCTCCCGTAGGAGT Control 20061126 Control_mouse__I.D._356
PC_481 ACCAGCGACTAG ZATGCTGCCTCCCGTAGGAGT Control 20070314 Control_mouse__I.D._481
PC.593 AGCAGCACTTGT YATGCTGCCTCCCGTAGGAGT Control 20071210 Control_mouse__I.D._593
PC.607 AACTGTGCGTAC YATGCTGCCTCCCGTAGGAGT Fast 20071112 Fasting_mouse__I.D._607
PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116
PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse__I.D._635
PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse__I.D._636
audy commented 10 years ago

From 8d691ac - need to prepend # at beginning of output file.

audy commented 10 years ago

Easier to just demultiplex myself. QIIME doesn't currently support our read format.