Since I am using a laptop, I'd like to exploit usegalaxy to perform an alignment using tophat. I succeeded in doing the alignment, but bowtie2 read half of the reads. The reads were generated by an Illumina Hiseq 2000, the protocol wasn't strand specific and it was a single end experiment.
- I performed a Fastqc test and the quality is ok;
- I use both the default index and one of my .fasta files to see if it is an index problem;
Do I have to change some setting to have all my reads read? Thanks in advice