Are we convert U to T in RNA before alignment?
Hi, I don't sure about the step of alignment my sequence with reference genome by minimap2. So I have the sequence data from RNA virus that contain U and I found the reference genome from this RNA virus in NCBI but in the genome have only T.
If I want to align my sequence and reference genome. I must be to convert U in my sequence before use minimap2 or this tools can automate convert U to T by itself?
1 answer
minimap2 can work with U's in query sequence.
$ more test.fa
>Test
GUAUUCUUGCCACGACUCAUCUCCAUGCAGUUGGACGAUAUCAAUGCCGUAAUCAUUGACCAGAGCCAAA
ACAUCCUACUUAGGUUGAUUACGAAACACGCCAACCAAGUAUUUCGGAGUGCCUGAACUAUUUUUAUAUG
$ minimap2 -a ref.fa test.fa
[M::mm_idx_gen::0.035*1.04] collected minimizers
[M::mm_idx_gen::0.046*1.49] sorted minimizers
@SQ SN:NODE_3_length_417179_cov_50.611328 LN:417179
[M::mm_idx_stat::0.051*1.45] distinct minimizers: 181299 (99.29% are singletons); average occurrences: 1.010; average spacing: 5.336; total length: 977396
Test 0 NODE_3_length_417179_cov_50.611328 1 15 140M * 0 0 GTATTCTTGCCACGACTCATCTCCATGCAGTTGGACGATATCAATGCCGTAATCATTGACCAGAGCCAAAACATCCTACTTAGGTTGATTACGAAACACGCCAACCAAGTATTTCGGAGTGCCTGAACTATTTTTATATG * NM:i:0 ms:i:280 AS:i:280 nn:i:0 tp:A:P cm:i:23 s1:i:131 s2:i:125 de:f:0 rl:i:0
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