Hello.
I am working on some RNAseq and received a few poor reads from our sample set. One possible undersatnding is cDNA contamination. note we aligned untrimmed reads because if there is "junk" in the read, then it will not align to the reference genome and automatically become omitted.
well what other possibilities could this be? My troubleshoot workaround is to trim the reads for quality and omit the adapters. Is it possible for adapter contamination in the prep kit?
if we remove the low quality reads, this might remove the entire read, or will it?
How has your team interpreted poor aligned reads? I will do a quality analysis to understand why the reads were mal-aligned. what are common things to look for?
I am working on some RNAseq and received a few poor reads from our sample set. One possible undersatnding is cDNA contamination. note we aligned untrimmed reads because if there is "junk" in the read, then it will not align to the reference genome and automatically become omitted.
well what other possibilities could this be? My troubleshoot workaround is to trim the reads for quality and omit the adapters. Is it possible for adapter contamination in the prep kit?
if we remove the low quality reads, this might remove the entire read, or will it?
How has your team interpreted poor aligned reads? I will do a quality analysis to understand why the reads were mal-aligned. what are common things to look for?
Comment