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.
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.
Comment