RobertsLab
pipeline for what doesn't align to a target?
wanting to see what doesn't align to seastar genome with my sea star RNAseq data
Almost all aligners have an option to save unaligned reads. Check options for whichever aligner you're using.
It seems like you're using HISAT2, so you'd use this option:
--un <path>, --un-gz <path>, --un-bz2 <path> Write unpaired reads that fail to align to file at
. These reads correspond to the SAM records with the FLAGS 0x4 bit set and neither the 0x40 nor 0x80 bits set. If --un-gz is specified, output will be gzip compressed. If --un-bz2 is specified, output will be bzip2 compressed. Reads written in this way will appear exactly as they did in the input file, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the input.
@grace-ac can you drop in a url to a
- genome file
- gff file
- gtf
- directory with trimmed reads
for any one of your species
