Question regarding the blacklist for specific genome builds

[bartcharbon]

Hi,

We're using "GCA_000001405.15_GRCh38_no_alt_analysis" as our reference genome build for analysis. Would the provided build 38 blacklist be suitable to be used with this reference build?

Kind regards, Bart Charbon

[philippesanio]

Hi @bartcharbon

Yes, you can use this reference in combination with the GRCh38 blacklist. All the blacklists we provide are based on the UCSC genome browser gap data. However, the blacklist_grch38_spectre.bed for example has been modified in difficult regions like the telomeric and centromeric regions.

Please keep in mind when running Spectre with a different reference file to not provide a MDR file. Spectre will generate a new MDR file with all the N regions for the specific reference in the output folder for you. The new MDR file can then be used with all other samples which have been aligned to the specific reference.

I hope this helps. Cheers, Philippe