Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: problems with PE reads upload
0
gravatar for pablinperaza
2.5 years ago by
pablinperaza • 0
pablinperaza • 0 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 • 594 views
ADD COMMENT • link •
modified 2.5 years ago • written 2.5 years ago by pablinperaza • 0
0
gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for pablinperaza
2.5 years ago by
pablinperaza • 0
pablinperaza • 0 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 COMMENT • link written 2.5 years ago by pablinperaza • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour