I have 5 time points of RNA-seq data which is paired end. In addition I have two samples (single end) one of which is replicate of 5 time points and One is separate additional time point. (I know it is an unusual situation- I have two samples in single read rest PE- long story short part of study was done by other grp). tMy questions are:
1. Should I keep separate PE and single reads and analyze separately, in that case how I will combine one of them as replicate.
2. Will that be OK if I combine both types of reads in that case will not I loose information if I follow single end.
3. Is there any rule which tool may be best to analyze such data, I was planning to use TopHat> Cufflink. Alternatively, I can think about DEseq.
My aim is to find differential expression transcripts an displacing events.
Thanks for your help and attention.
1. Should I keep separate PE and single reads and analyze separately, in that case how I will combine one of them as replicate.
2. Will that be OK if I combine both types of reads in that case will not I loose information if I follow single end.
3. Is there any rule which tool may be best to analyze such data, I was planning to use TopHat> Cufflink. Alternatively, I can think about DEseq.
My aim is to find differential expression transcripts an displacing events.
Thanks for your help and attention.
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