anybody know what the 4 non-ACGUT characters are in Gencode 38 transcript file, if they do exist?

Question

[nathan bowen]

got this from kallisto when indexing gencode.v38.transcripts.fa

warning: replaced 4 non-ACGUT characters in the input sequence with pseudorandom nucleotides

thoughts?

Answer 1

[dsull]

There are bases labeled N in that file. So kallisto will replace them with random valid nucleotides (i.e. A, T, C, or G).

Given that the N bases only occurs 4 times in that ginormous file, it really won't affect anything.

[nathan bowen]

right, I was just curious as to how 4 Ns snuck in.....thanks.

[Ram]

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