RNA-seq data analysis with 40bp reads

heytreeful

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Join Date: Oct 2011

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RNA-seq data analysis with 40bp reads

10-17-2011, 10:23 AM

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
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Jon_Keats

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Join Date: Mar 2010

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10-17-2011, 09:30 PM

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
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RNA-seq data analysis with 40bp reads

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