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I have 454 data from cDNA sample. If I would like to report the number of reads of every isotig/contig, is it a correct way first to check the number of reads/contig from 454Allcontigs.fna. And after that check from the 454Isotigs.txt file which contigs forms an isotigs and sum the reads? What ways do you use? Is this a good way to report the most abundant transcripts?
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I understand.
Which way would you determine the most abundant transcripts? Is this possible? Can you ever use the number of reads?Comment
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A really crude way would be to divide number of reads (for a contig) by contig length. But, using real statistics (FPKM and all that) gives a much more reliable answer.Comment
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real statistics
Can you recommend any good articles about how this statistical work has been done?Comment
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