I'm a newbie in analyzes with RNA-Seq.
I have paired-end reads data (Sanger / Illumina 1.9) and would like to cut the reads using quality score.
We have visualized data with FastQC and we tested the softwares: sickle, Spade, fastq quality filter (fastx) and AllPaths.
The best result was obtained with the fastq quality filter, but we lost a lot of reads in the process (it does not cut off part of the reads, only excludes the entire read).
I wonder if there is already a program that recognizes the first occurrence of a symbol (eg '#') and cuts the sequence and the quality from that point.