Question: How To Merge Multiple Fastq Files
gravatar for Jennifer Hillman Jackson
7.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Tracy, The tool "Text Manipulation -> Concatenate datasets tail-to-head" can put the two together. Then set the datatype to fastq, if needed (click on the "pencil" icon for the full dataset to reach the "Edit Attributes" form to make the change). Be sure to watch out for an extra newline being added between the two files. You can test for/eliminate this using "Filter and Sort -> Select" with the options "that: NOT Matching" and "the pattern: ^$". (the regular expression '^$' [no quotes] matches empty lines). I am sending to the galaxy-user mailing list for our internal tracking and for other users to learn from. Please send all questions directly to the list going forward, it is very helpful for us. Thanks for using Galaxy! Jen Galaxy team much! -- Jennifer Jackson
galaxy • 1.2k views
ADD COMMENTlink modified 7.1 years ago by Kevin150 • written 7.1 years ago by Jennifer Hillman Jackson25k
gravatar for Kevin
7.1 years ago by
Kevin150 wrote:
Hi Jennifer, just out of curiousity, is the command a linux cat? or does it actually parse the fastq sequences? asking as my service provider actually just split my PE files by lines (not no. of reads ) in fastq assuming that I can't merge them in galaxy, I am merging them properly then splitting them again (anyway i can map using concurrent processes and merged the bam later on Cheers Kevin
ADD COMMENTlink written 7.1 years ago by Kevin150
Hello Kevin, This particular function is like a "cat" - will work any text file. Assuming that you run the function in the same order the data was split, it should merge fine. Should you want to work with tools that manipulate FASTQ files specifically, a tool search of "FASTQ" will bring up most plus look under the tool group "NGS: QC and manipulation -> Generic FASTQ manipulation". And in case you didn't see this, data can be uploaded using FTP. Several compressed formats are support. Using a desktop client can the track progress of, restart, and confirm a load. Best wishes for your project, Jen Galaxy team -- Jennifer Jackson
ADD REPLYlink written 7.1 years ago by Jennifer Hillman Jackson25k
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