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.
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.
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