Concatenate fastq files in galaxy

Question: Concatenate fastq files in galaxy

2.9 years ago by

biorashid • 0 wrote:

Hi, I have several fastq files that I want to merge. can anybody share how to concatenate multiple files in One file in galaxy?

concatenate galaxy datatype text-manipulation • 1.6k views

ADD COMMENT • link •

modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by biorashid • 0

When I try 'concatenate datasets in Text Manipulation', the following appears.

"This is a batch mode input field. A separate job will be triggered for each dataset." and multiple datasets appear from each fastq file. I want to merge all in one big file.

ADD REPLY • link written 2.9 years ago by biorashid • 0

Don't use the 'multiple dataset' icon, stay on 'single dataset', and add the individual fastq files by clicking on "inser dataset" as oftne as requeired and then select the file individualy

ADD REPLY • link written 2.9 years ago by Hotz, Hans-Rudolf • 1.8k

Thanks..that was helpful. .. Best

ADD REPLY • link written 2.9 years ago by biorashid • 0

2.9 years ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

Have a look at "Text Manipulation -> Concatenate datasets"

Regards, Hans-Rudolf

ADD COMMENT • link written 2.9 years ago by Hotz, Hans-Rudolf • 1.8k

5 months ago by

palumbor • 0

palumbor • 0 wrote:

I am having difficulty using Concatenate. When I try to concatenate fastq.gz datasets corresponding to different flow cells (datasets 1 to 4), the ~200 MB datasets are concatenated into an ~2 KB fqtoc file, instead of a larger (I'd guess ~800 MB?) fastq.gz file. Consequently, the concatenated file (which doesn't appear to be concatenated at all) cannot be used, for example, in fastqc (which of course requires at least that a fastq.gz file be the input). Any help would be greatly appreciated.

ADD COMMENT • link modified 5 months ago • written 5 months ago by palumbor • 0

Hi, I encountered the same problem. Have you solved it yet? Under "text manipulation", there are 2 concatenate: - 1.) Text manipulation -> concatenate datasets tail-to-head 2.) Text manipulation -> concatenate datasets tail-to-head (cat)

The 1st one is galaxy version 1.0.0 and the 2nd one is galaxy version 0.1.0. You might be using the 2nd one and ended up with the fqtoc file. Try using the 1st one. It worked for me.

ADD REPLY • link written 5 months ago by hadiaziz • 20

Hello, Only plain text uncompressed data can be used with Concatenate. Uncompressed the data, concatenate, then compressed the result if you want to work with it that way. The initial and intermediate datasets can be permanently deleted (purged) to recover account quota space once you know that data works with downstream tools.

FAQs: https://galaxyproject.org/support/#troubleshooting

How do I find, adjust, and/or correct metadata? https://galaxyproject.org/support/metadata/
Checking for active vs deleted vs permanently deleted (purged) datasets and histories https://galaxyproject.org/learn/managing-datasets/#delete-vs-delete-permanently

ADD REPLY • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »