Can you concatenate gz files

Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Log In. Log In Sign Up About. How To Merge Two Fastq. Gz Files? Entering edit mode. How to find and merge all fastq files into one log file. Pierre Lindenbaum k. Note that you can confirm that this works in most cases by doing something like the following: cat file1.

So in order to do that, I would have to list each sample twice, and name them something unique, yes? Do you think that worth it? If you do not see any differences between runs, then you are safe to merge and use your original metadata file with sample IDs S1, S2, etc. Batch effects can be a serious issue; there has been a lot of talk about batch effects elsewhere on the forum … those posts will offer good rationale for the need to check for batch effects, how to test, and how to merge.

Fortunately for you, you are just trying to collect more data not compare between samples sequenced on separate runs so if worse comes to worse you could always just use one run if there are irreparable batch effects…. So I should summarize a feature table while excluding sequences based on sampling depth, then test for the batch effect.

If there is none, I should combine the files based from the 2 runs, then tabulate the table to give the DNA sequences for each sample. Does that sound reasonable? If so, I may reach out to troubleshoot the command line for doing so…. See the search results I linked to above — there are lots of ideas that colinbrislawn and others have put forth on other forum posts.

As a general batch-effect-testing protocol:. I am now not able to even import the files which should have nothing to do with the metadata file, correct? I am inputting-. I am thinking it has to do with the barcode identifier or lane number? Please help this newbie, and thanks for your patience! Combining fast. I am trying to combine 2 separate runs of samples into one, and am using the following gzcat file1.

Thanks for any insight! Hello David, Yes! Let me know if this works for you! Demultiplexing and Trimming Adapters from Reads with q2-cutadapt. Colin, Thanks for your reply! Ah ok! That doesn't answer my question. I need single uncompressed file that is concatenation of those two files. Show 1 more comment. Active Oldest Votes. Surprisingly what Quanta posted in the comments works -- at least on my Mac!

Improve this answer. Yup, it's intentional. I find such behavior disturbing Add a comment. Bgs Bgs 2 2 silver badges 5 5 bronze badges. You can try this: tar cvf combined. To uncompress the file, you can try: tar -xavf combined.

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