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CustomProDB (version 1.22.0)

Will you select a genome annotation from your history or use a built-in annotation?:

See `Annotations` section of help below

Select genome annotation:

If your genome of interest is not listed, contact the Galaxy team

BAM file:

VCF file:

Annotate SNPs with rsid from dbSNP:

The genome annotation must have been prepared with dbSNP.

Annotate somatic SNPs from COSMIC (human only):

The genome annotation must have been prepared with COSMIC.

Transcript Expression Cutoff (RPKM):

If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database.

Create a variant FASTA for short insertions and deletions:

Create SQLite files for mapping proteins to genome and summarizing variant proteins:

Create RData file of variant protein coding sequences:

The PSM2SAM tool needs this to map variant proteins to genomic locations

Description

Generate custom protein FASTAs from exosome or transcriptome data.

The reference protein set can be filtered by transcript expression level (RPKM calculated from a BAM file), and variant protein forms can be predicted based on variant calls (SNPs and INDELs reported in a VCF file).

Annotations CustomProDB depends on a set of annotation files (in RData format) to create reference and variant protein sequences. Galaxy administrators can use the customProDB data manager to create these annotations to make them available for users.