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Old 10-23-2010, 08:09 PM   #1
kentnf
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Location: Ithaca

Join Date: Jan 2009
Posts: 26
Default Different results produced by tophat?

I use tophat to map my strand-specific RNA-seq seqs and its reverse complementary seqs to genome, but the results have a little difference.

For example, I have 5700000 seqs in one sample after sequencing, 5000000 of them mapped to genome by tophat. For reverse complementary seqs, maybe 4998000 of them were mapped to genome.

command I used:
$tophat -o output1 --segment-mismatches 0 genome_index RNA-seq.fa

Then I compare mapped seqs of different results. There are 50000 seqs in the results A (5000000 mapped, normal strand) are not present in result B (4998000 mapped, reverse complementary strand). Another 50000 seqs are not present in result A but included in result B.

Who can tell me why the results is different ? Thanks.
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