Hello, I'm new in analyzing RNA-seq data and I need to process several sampled sequenced by AB SOLiD system in paired end mode (SRR1175538). These fastq files are not similar to Illumina fastq,
1. Reads length are not the same in forward and reverse fastq, read length of forward is 75nt while the reverse is 35nt
2. Many reads in the reverse fastq file are
Should I trim these reads before alignment and what tool should I use? And what aligner should I use for reads mapping? Can I just use STAR or hisat2 in their PE mode?
Thanks a lot.