SICER is not available for the genome.

[moonmoondeb]

Hi
I want to use the SICER tool for my histone chip-set analysis. But its showing “SICER is not available for the genome.”
I am using Chicken genome assembly GRCg7b. (NCBI RefSeq assembly
GCF_016699485.2 and Submitted GenBank assembly
GCA_016699485.1).
If this genome assembly is not available for the tool, how can I make it available.
Kindly help me.
With regards
Moonmoon

[jennaj]

Hello @moonmoondeb

For how to include your own genome for use with tools, please see the guides below.

@jennaj

Try using the custom genome feature.

FAQ: How to use Custom Reference Genomes?

If you need to assign a database metadata to datasets, your custom genome can be promoted to a custom build.

FAQ: Adding a custom database/build (dbkey)

---

With that context, to answer your question here

@moonmoondeb

I want to use the SICER tool for my histone chip-set analysis. But its showing “SICER is not available for the genome.”
I am using Chicken genome assembly GRCg7b. (NCBI RefSeq assembly
GCF_016699485.2 and Submitted GenBank assembly
GCA_016699485.1).
If this genome assembly is not available for the tool, how can I make it available.

The solution would be to create a Custom Build database key for your genome, and to assign that to your input datasets. This will allow the tool to access the fasta index for your genome (to interpret scientific options like Effective genome fraction).

Be sure to carefully read that guide: format your genome fasta in a simple way, and create a unique database key that is all oneWord with no special characters, as an example GCA016699485 should work fine.

Do not reuse any existing server database key or expect problems.

---

For related topics here at this forum, including more help with troubleshooting how these work, please see custom-genome and custom-build .

Any questions you may have, please ask and we’ll try to help more.