Genome reference for alignment

Question

[vicenmart]

Hello everyone, I'm analyzing MiSeq results with Chipster, I am stoked at the alignment step because I need to use an available rodent sequence but when I open the "genome" box, all the sequences available in that box are not the one I need. How do I include that sequence in the box? Sorry that English is not my mother language, I hope you can understand and help. Great to be here and I will be glad to help anyone with some comments and recommendations as well.

Answer 1

[Chipster]

Hi there,

you can use the "own genome" versions of the tools (for example instead of "TopHat2 for paired end reads", use "TopHat2 for paired end reads and own genome").

For this tool, you need to import your reference genome to Chipster in .fasta format. You can use "File" -> "Import files" or "File" -> "Import from". If your genome is in Ensembl, you can use the tool Utilities / Retrieve data for a given organism in Ensembl.

Hopefully this was helpful!

With best regards, Maria / Chipster team