Hi. I am new in galaxy and I am having problems when uploading samples. I am uploading PE reads (R1 and R2), using Pear for pairing sets, concatenate datasets (have files w/6Million reads each) to have a unique file (around 30 millon reads) and then I performed FASTQC to that file. The FastQC report says that I have much more reads, and when I performed FASTQC just to one R1 sample it reports just 10% of the reads. Why it happens? Do I need to set any parameters to import? Thank you if you can help me. Kind regards, Pablo
It is okay to upload paired datasets from this tool. However, do not concatenate multiple samples. Leave each distinct when loaded. Use FTP to make this simpler to organize when uploading or if any data is over 2 GB in size. https://wiki.galaxyproject.org/Support#Loading_data
Once the data are loaded, the issues with the tools should go away. Consider using a Dataset Collection and a Workflow (once the analysis path is known).
- https://wiki.galaxyproject.org/Histories - Section 6
Thanks, Jen, Galaxy team
Hi Jennifer, thank you for your reply and the tutorials. They were very helpful.
Now my question is, when I get this results from tha paired reads, hoy can I merge them. Some facilities give me reads files in no more than 6millon reads, and they give me always more than 6 files per sample.
XX_L001_R1_001 XX_L001_R1_002 XX_L001_R1_003 XX_L001_R2_001 XX_L001_R2_002 XX_L001_R2_003
At the End I will have
XX_001 XX_002 XX_003
But, I would like to have XX (all paired reads in one file). Is it possible? In order to handle less files. Thank you. Pablo