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
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
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