Hi,
I'm classifying samples with a database I created from combining several refseq databases (including the mammalian database).
I notice that in many instances I have many reads assigned to a higher order but few reads assigned to lower orders.
For example here is a part of the report file:
0.01 71 5 C4 314145 Laurasiatheria
0.01 66 17 O 33554 Carnivora
0.01 48 12 O1 379583 Feliformia
0.01 36 33 F 9681 Felidae
0.00 3 2 F1 338152 Felinae
0.00 1 0 G 9682 Felis
0.00 1 1 S 9685 Felis catus
0.00 1 0 O1 379584 Caniformia
0.00 1 1 F 9608 Canidae
So here I see 36 reads assigned to Felidae Family, but only 1 read is assigned to a specific species under that family.
Is there any reading resource available on that topic? (I didn't find anything to read about it, but perhaps I didn't formulate my question correctly)
What does that mean and how do reads get aligned to a high taxon rather than a specific species?
Hi, I'm classifying samples with a database I created from combining several refseq databases (including the mammalian database). I notice that in many instances I have many reads assigned to a higher order but few reads assigned to lower orders. For example here is a part of the report file: 0.01 71 5 C4 314145 Laurasiatheria 0.01 66 17 O 33554 Carnivora 0.01 48 12 O1 379583 Feliformia 0.01 36 33 F 9681 Felidae 0.00 3 2 F1 338152 Felinae 0.00 1 0 G 9682 Felis 0.00 1 1 S 9685 Felis catus 0.00 1 0 O1 379584 Caniformia 0.00 1 1 F 9608 Canidae
So here I see 36 reads assigned to Felidae Family, but only 1 read is assigned to a specific species under that family.
Is there any reading resource available on that topic? (I didn't find anything to read about it, but perhaps I didn't formulate my question correctly) What does that mean and how do reads get aligned to a high taxon rather than a specific species?