[galaxy-user] Troubles with Bowtie alignement of sRNA dataset (against precursor of mirBase)

Hi people, I have a litle problem with Bowtie alignments. I am tryin to align sRNA Illumina dataset to hairpin mirbase. The problem is that after the steps (detailed below) I only obtain reads of 15-18nt, and I know that I have a lot of microRNAs (20-22nt) in my data. Beside the size problem,

Re: [galaxy-user] filtering fastq file according to qual score

Hi Haluk, It is definitely not conventional to remove bases that have low quality, because this disrupts the DNA sequence and may introduce frameshifts. It is typically better to trim the ends of the sequence, or to remove it altogether if its quality does not match your requirements.