RNA References

RNA Alignment

HiSAT Databases

HiSat Public Indexes

• Note to use these, the files will have to renamed with the prefix genome

To Build an Index

hisat2-build  genome.fa genome

StarFusion

Human Ref: CTAT plug and play

BAM Read Count

mkdir references
cp GRCh38.fa references/genome.fa
tar cfz ref.tar.gz references

Panel Reference

tar cfz panel.tar.gz targetpanel.bed

Exon Skipping and Gene Abundances

Gencode

• https://www.gencodegenes.org/human
• https://www.gencodegenes.org/mouse