Maize Endopserm RNAseq: Cufflinks

[Siva]

Hello
I have performed maize endosperm RNA seq. I have a total of 48 seq reads (24 samples at two lanes each) to cover. These are all GAII reads. I am mailing because I am confused about Cufflinks input.

I built a bowtie index of the maize genome. I then ran Tophat, for which I used the index as the reference and supplied four (two samples x two lanes) of my sequences from a flow cell. I got the desired output, accepted_hits.sam. This describes every hit to each of the sequences that I supplied. Now can I use this combined (all four reads against the maize genome) accepted_hits.sam input for Cufflinks? Should I have run Tophat on each 'sequence read' separately, or is there a way Cufflinks parses the tophat output (accepted_hits.sam) for each read?

Any suggestions?

thanks
Siva
Columbia, MO

[Boel]

Tophat should be run for each sample separately, cufflinks is also run for each sample separately. Then cuffcompare is run on all samples at once, and used to track Cufflinks transcripts across multiple experiments and, optionally, compare the assembled transcripts to a reference annotation.

Hope this helps.

Boel

[Siva]

Thanks a lot Boel. I will run them separately for each sample.

Siva