Dealing with paired fastq reads

July 19, 2022 update:
OK, I’m trying to reinstall PEAR on my new-ish laptop and running into errors. After struggling a bit, I decided to switch over to using Fastq-join. This is way easier to install and run, as you can see below:

Based on the information on this website, and assuming you have anaconda installed, run:
conda install -c bioconda fastq-join

After that, actually pair your files running a command like:
fastq-join ACE2-Kozak-mini-library-pooled_R1_001.fastq ACE2-Kozak-mini-library-pooled_R2_001.fastq -o ACE2-Kozak-mini-library-pooled.fastq

Note 1: You can run fastq-join on gzipped files, like so:
fastq-join No-infection-maybe_R1_001.fastq.gz No-infection-maybe_R2_001.fastq.gz -o No-infection-maybe.fastq.gz

Note 2: If working with gzipped fastq data, it’s a little trickier to look at your files compressed files. To look at the first read, for example, you need to use a command like this:
gunzip -c SARS2-MOI-0pt1-1_R1_001.fastq.gz | head -4

Here’s the original (now deprecated) text in this post:

Got some paired Illumina sequencing back today, and wanted to pair the R1 and R2 fastq files. I vaguely remember using PEAR to do this before, so gave it a shot. Since the files are relatively small, I figured I’d just try to run this locally, which meant trying to install it (and it’s various dependencies) on my Macbook. Here are the steps…

  1. Download “autoconf-2.65.tar.gz” from this website. Uncompress it, and then go into the now uncompressed directory, and type in “./configure && make && make install”

2. Download “automake-1.14.1.tar.gz” from this website. Uncompress it, and then go into the now uncompressed directory, and type in “./configure && make && make install”

3. Get PEAR academic from this website by entering in your info, receiving an email, and downloading “pear-src-0.9.11.tar.gz”. Uncompress it, and then go into the now uncompressed directory, and type in “./configure && make && make install”

Huzzah. It should now be installed.

Now you can go to whatever directory has your R1 and R2 files, and type in something like so:
“pear -f KAM-IDT-HM_R1_001.fastq -r KAM-IDT-HM_R2_001.fastq -o IDT_HM”

You should now have a file called “IDT_HM.assembled.fastq” that has all of the joined paired reads.

5/18/21 Update: I was working on something else that required trimming reads. I decided to use fastp to do this. The instructions to install fastp is as follows (essentially following the instructions here):

  1. Download the zip file (under the “Code” button) from https://github.com/OpenGene/fastp, and unzip it.
  2. Use terminal to go to the directory that is made, and run
    $ make
  3. Run the following command:
    $ sudo make install
    … and then type in your computer password when prompted. Fastp should now be installed.