Paired End for Stacks and UNEAK

Both stacks and uneak are made for single end reads. If you have paired end data here is a little cheat that puts “fake” barcodes onto the mate pairs and prints them all out to one file. It also adds the corresponding fake quality scores.

perl BarcodeFile R1.fastq R2.fastq Re-barcoded.fastq

BarcodeFile should look like (same as for my demultiplexing script) spaces must be tabs:
sample1 ATCAC
sample2 TGCT

# note this could also look like this:

As it does not actually use the names (it just looks at the second column).

Here it is:

posting code, a warning (Greg B.)

I’ve just noticed there is a problem with code that has been dropped into posts. If you copy and paste directly from the post, for some reason, depending on the syntax of the code you may lose important bits. For example “while ()” appears as “while ()” but thats not what it is! Click on edit and see for yourself! You will not have this problem if you go to the edit post page and copy from there. Also and this may just be the text editor I use but some commented line were broken into multiple lines which did not have ‘#’.

There has to be a better way to host code here but I don’t know what it is. Any ideas?

How to post – code (Dan E.)

We have a problem sharing code via RLR.

The Problem

Unfortunately WordPress has a list of acceptable file types that it allows to be uploaded to our media library and none of the useful coding file types are on that list. The list is simply a list of acceptable file extensions. This means if you write a useful R script (or perl or python) script and save it with a standard file extension, like .R or .pl, WordPress will not allow you to upload it to the RLR media library so that you can share it via a post.

The Solution

The list of acceptable file extensions can be hacked and I might give it a try but, until I do, you will have to do one of these things:

  • Change the file extension. If you save your script as a .txt file it will upload fine. You should make it clear in your post what kind of script it is and then people who download it can change the .txt extension to whatever they want.
  • Put the code in your post. If your script is not too long you can simply copy and paste the code from your text editor into the post editor. The formatting of the code will remain true to the original so users can simply copy and paste it back out into a text editor or R-Studio or wherever. See Rose’s post about plotting STRUCTURE results for an example of this.
  • Compress your script file. If your script is big you can try zipping it and then uploading the compressed file. Users can then just download and unzip it. [As of November 2011 this hasn’t been tested.]

Dan E.