RNA-seq data analysis with 40bp reads

[heytreeful]

Hi everyone,

I am preparing to analyze some 40bp RNA-seq data generated by Illumina HiSeq from mouse samples. It seems that most RNA-seq tools nowadays are optimized for long sequence reads (>75bp) and paired-end reads.
Can I still use TopHat and Cufflinks for these 40bp reads? Is it possible to perform transcriptome assembly with limited splice reads? Since the mouse genome is well annotated, can I get by without transcriptome assembly since the goal of our study is not to discover novel genes but just to detect differential expression of known genes? I am new to this; any suggestions/comments will be much appreciated! Thank you.

p.s. sorry for double posting if you saw this message in the "Illumina" forum already; I thought the bioinformatics forum might be more suitable place so I re-posted

[Jon_Keats]

Check out some of the HT-seq and DESeq tutorials, most of that set of tools is designed for this read format and works very well