Gobyweb allows you to upload a .tsv (tab separated values) file along with your samples. This .tsv file provides you with fine grained control when uploading multiple samples and/or paired-end reads. Assuming the string ” | ” below is a single tab character, an example of the contents of this file would be
sampleName | filename | pairIndicators | pairing 30reads_a | 30reads_a1_1.fq | _1,_2 | 0 30reads_a | 30reads_a1_2.fq | _1,_2 | 1 30reads_a | 30reads_a2_1.fq | _1,_2 | 0 30reads_a | 30reads_a2_2.fq | _1,_2 | 1 30reads_b | 30reads_b_1.fq | _1,_2 | 0 30reads_b | 30reads_b_2.fq | _1,_2 | 1 30reads_c | 30reads_c.fq
The .tsv file you provide has the following properties:
- The file should contain a header line. The four columns that can exist are sampleName, filename, pairIndicators, pairing. The order of the columns is unimportant.
- The columns pairIndicators and pairing are optional. If your samples are not paired end, you don’t need to include these columns at all (including the header line). If some of your samples / files are not paired, you can omit values for these columns on those lines.
- If not provided, the value for any row of pairIndicators is “_1,_2”. In the examples above the “_1,_2” say the filename will contain a “_1” or a “_2” toward the end of the filename. Other common values for pairIndicators are “_r1,_r2” or “_r0,_r1”.
- If not provided, the value for any row of pairing is “0”. “0” means this file represents the first file in a pair. “1” means this file is the second file in a pair. The two files making up a pair should have the exact same number of reads.
- The above example indicates you are uploading seven fastq files along with the .tsv file. These seven fastq files will create 3 individual samples. These samples will have the names “30reads_a”, “30reads_b”, “30reads_a”.
- “30reads_a” and “30reads_b” will be paired-end samples. “30reads_c” will not be paired-end.