<p>Hello everyone!</p>

<p>I&#39;m a newbie in analyzes with RNA-Seq.<br />
I have paired-end reads data (Sanger / Illumina 1.9) and would like to cut the reads using quality score.<br />
We have visualized data with FastQC and we tested the softwares: sickle, Spade, fastq quality filter (fastx) and AllPaths.<br />
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).</p>

<p>I wonder if there is already a program that recognizes the first occurrence of a symbol (eg &#39;#&#39;) and cuts the sequence and the quality from that point.</p>

When a major part of the read has low quality bases then trimming reduces the length of the read and now the read can't be aligned with higher confidence against the reference genome. So almost all the trimming software will discard reads whose length has been reduced to less than some number (say n=30). If most of your reads suffer from this problem than all the trimming tools will behave in the same way i.e. discarding majority of the reads. Although this is not a solution but I would suggest you trying [Trimmomatic][1] and see if it helps.

 [1]: http://www.usadellab.org/cms/?page=trimmomatic