Completed on 28 Jul 2018 by Hiroaki Sakai.
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This manuscript describes the new open access data analysis platform, Rice Galaxy, based on Galaxy framework. It is of great importance to provide the service like this to make full use of the genotyping and phenotyping data derived from the 3k rice genomes project. I had no comments on the manuscript, but several issues related to the content of the Rice Galaxy. Please note that the following comments are based on the trial from the URL http://188.8.131.52:8080/, not http://galaxy.irri.org/.
1. Since users are not necessarily familiar with the variety IDs such as 'B001' and 'IRIS_313-10000', variety names such as 'Heibiao' and 'SUWEON 311' should be acceptable. It would be very user-friendly if Rice Galaxy converts any variety names into corresponding unique IDs.
2. It seems that only MSU gene IDs are valid to specify gene locus. If so, RAP gene IDs should also be acceptable.
3. Is there any reason for why only SOLiD data is subject to QC and manipulation tools? If Rice Galaxy outputs fastq files and/or enables users to analyze fastq files, additional tools such as QC (e.g. FASTQC), mapping to reference, and variant calling should be implemented. Otherwise, it would be better to omit the 'NGS: QC and manipulation' tools.
1. When users select 'Yes' for 'Filter SNP based on subpopulation' item in the 'RAVE' tool, more than one subpopulations should be able to be selected.
2. The usage of the tool 'FROM 3K RICE PROJECT - Get Subset of 3K' tells to use 'convert formats-convert BCF to VCF tool' for further analyses, but such tool is not available in the toolbox. Is 'BCFtools-bcftools view VCF/BCF' the one?
3. The tool 'Oghma' was not found in the toolbox. Is 'Genomic Prediction' the one?