Question: problems with PE reads upload
0
gravatar for pablinperaza
20 months ago by
pablinperaza0 wrote:

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

rna-seq • 389 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by pablinperaza0
0
gravatar for Jennifer Hillman Jackson
20 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

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).

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 20 months ago • written 20 months ago by Jennifer Hillman Jackson24k
0
gravatar for pablinperaza
20 months ago by
pablinperaza0 wrote:

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

ADD COMMENTlink written 20 months ago by pablinperaza0
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