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:
https://academic.oup.com/bioinformatics/article/34/17/i884/5093234
fastp GitHub:
https://github.com/OpenGene/fastp
Example Files:
https://github.com/ACSoupir/Bioinformatics_YouTube/tree/master/Raw%20Reads/files
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