Bioinformatics - fastp FastQ Preprocessing Tool (Timestamps)

Welcome back, Everyone. Today I'll talk about fastp which is useful for processing raw FastQ files before using them with an aligning tool like STAR or Bowtie2. Here I quickly go through the different options and uses for fastp. While I haven't used it in the past, I think I'll use it in the future!
00:41 - fastp is useful
01:15 - installing fastp with miniconda `conda install -c bioconda fastp`
02:05 - RNA-Seq files `wget -i readlist.txt`
03:26 - running fastp
03:33 - fastp help `fastp --help`
03:51 - input files `-i/o` and -I/O`
05:30 - removing short reads `-l`
06:19 - adapter trimming
09:54 - sliding window quality trimming
14:09 - base correction `-c`
16:35 - poly 'G' trimming `-g/G`
17:57 - UMI processing `-U`
19:22 - overrepresented sequences `-p/P`
21:12 - interleaving paired end read files `-m`
fastp: an ultra-fast all-in-one FASTQ preprocessor:
academic.oup.c...
fastp GitHub:
github.com/Ope...
Example Files:
github.com/ACS...
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