Question: Merging two fastq files together
gravatar for yenaoh90
3.3 years ago by
yenaoh900 wrote:

Hi all,

I've recently received the .fastq files for my rna-seq experiment. According to the sequencing centre, "the samples were run across 2 lanes," and I have received 2 single read .fastq files for each sample.

1) Can somebody explain what it means by "run across 2 lanes"? 

2) Does "concatenate datasets tail to head" combine the two files by "merging" the two files on top of each other, or by "connecting" file 1 and file 2? In my case, how would I go about combining the two files before moving onto alignment using Tophat? 

Thank you in advance,

rna-seq galaxy • 3.2k views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by yenaoh900
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The term "two lanes" refers to how the sample was physically sequenced by the lab. Section 1 of the Galaxy NGS 101 could be helpful to review. If you want more information, there are many other online resources, just google the technology terms.

The Concatenate tool merges data files together by "stacking" one on top of another. It would be an appropriate choice for your case. If you want to understand exactly how the tool works, take a few smaller files with sequence names that you can recognize and run the tool as a test with them.

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Jennifer Hillman Jackson25k

Thank you so much Jen for the clarification.


ADD REPLYlink written 3.3 years ago by yenaoh900
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