You should check out the data importing tutorials here. In particular, see the section on fastq manifest formats and casava8 format— you will either need to provide a manifest file to map your sample identifiers or specify the source type if you plan to use a different importing scheme. By default, the importer is assuming that you are following the manifest format but you have not provided a manifest file to this command.
Thanks for your prompt reply, I am working on my own dataset and the data is already in my working directory any idea as to how i should convert them in the required formats? Please advise.
Hi @kedi,
The import method will depend mostly on how your samples were prepared and sequenced. Please read those tutorials first to determine what works for the formats that you have (you probably don't need to convert anything, you just need to determine whether your sequences are in a single file or one file per sample)
If you are still having trouble, could you please share the following:
the output of ls /scratch/sysusers/kedibone/reanalysis
what do your sequences look like? Could you show me the first few lines of an example sequence file and an example barcode file? (e.g., if your file is file.fastq, use head file.fastq. If it ends in .gz, use gunzip file.fastq.gz | head)
what library prep and sequencing protocol did you use?
BCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFEFFGEEFEGFGDDGFGGGGGFGFGGDECGGGGFGGGGGGBFGFGGGGGGGFGGGGGGGGGGGGGGGGFGGGGDEFGGFGGCCCCGEGGGGGGGGGGG=E=8EFFG8EGGDBFEEGGGGFGGGF(97C8EG275@;B54DC5>843FD@7?FFF>F;73,8<??FD70+CG=C0(7<??80;#247506)8*+<4CF
3. MiSeq flow cell for a 2 × 300 paired-end sequencing
thanks in advance