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Novoindex error with gene masked genome

Hi there,

When I try to build transcriptome index using gene masked genome, I got error message:
Error: Invalid NA code in ~/MaskedFastas/geneMaskedGenome.fasta at line 1.

I built gene masked genome using Useq MaskExonsInFastaFiles as:
java -Xmx8G -jar /usr/local/useq/Apps/MaskExonsInFastaFiles -f ~/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes -u ~/refFlat_clean.txt -s ~/MaskedFastas

Any idea how to fix it?
Thank you,

Shile


Hi Shile,

Could you post 2 or 3 lines of the masked fasta file so I can see how it's masked.

Novoindex supports masking of lower case nucleotides. Masked nucleotides could also be encoded as Ns'

Colin


This problem was resolved by the user. It was likely a file formatting problem with the masking program.
Colin


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