Question: Concatenate fastq files in galaxy
0
gravatar for biorashid
2.9 years ago by
biorashid0
biorashid0 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? 

 

ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 2.9 years ago by biorashid0
1

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 REPLYlink written 2.9 years ago by biorashid0
1

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 REPLYlink written 2.9 years ago by Hotz, Hans-Rudolf1.8k

Thanks..that was helpful. .. Best

 

ADD REPLYlink written 2.9 years ago by biorashid0
4
gravatar for Hotz, Hans-Rudolf
2.9 years ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:

Hi

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

 

Regards, Hans-Rudolf

ADD COMMENTlink written 2.9 years ago by Hotz, Hans-Rudolf1.8k
0
gravatar for palumbor
5 months ago by
palumbor0
palumbor0 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 COMMENTlink modified 5 months ago • written 5 months ago by palumbor0
1

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 REPLYlink written 5 months ago by hadiaziz20

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

ADD REPLYlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
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