current RIMA Kraken version

Author: Lin Yang

RIMA.snakefile

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+### We have prepared the RIMA reference folder with the current version we used. You can directly download from Iris server:
+
+```
+# We have nearly 69G reference files
+
+wget http://cistrome.org/~lyang/ref.tar.gz 
+
+```
+
+
+# Steps to make your own custom reference files for RIMA pipeline
+
+### Reference fasta
+
+The human GDC hg38 fasta file is downloaded from [GDC website](https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files). 
+
+### Gene annotation file (gtf)
+
+The human gtf annotation file is downloaded from [GENCODE website](https://www.gencodegenes.org/human/). The current annotation file we used is V27.
+
+
+### build STAR index
+
+```bash
+conda activate rna
+
+## STAR Version: STAR_2.6.1d
+STAR --runThreadN 16 --runMode genomeGenerate --genomeDir ./ref_files/v27_index --genomeFastaFiles GRCh38.d1.vd1.CIDC.fa --sjdbGTFfile gencode.v27.annotation.gtf
+...
+00:04:54 ..... started STAR run
+00:04:54 ... starting to generate Genome files
+00:05:57 ... starting to sort Suffix Array. This may take a long time...
+00:06:11 ... sorting Suffix Array chunks and saving them to disk...
+00:17:43 ... loading chunks from disk, packing SA...
+00:19:31 ... finished generating suffix array
+00:19:31 ... generating Suffix Array index
+00:23:20 ... completed Suffix Array index
+00:23:20 ..... processing annotations GTF
+00:23:35 ..... inserting junctions into the genome indices
+00:26:49 ... writing Genome to disk ...
+00:27:06 ... writing Suffix Array to disk ...
+00:28:53 ... writing SAindex to disk
+00:29:05 ..... finished successfully
+```
+### RSeQC reference files
+
+We download the human annotation bed file including the whole genome bed file, and house keeping bed file from RSeQC page from [sourcforge website](https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/).
+
+```bash
+./ref_files/refseqGenes.bed
+./ref_files/housekeeping_refseqGenes.bed
+```
+
+### build salmon index
+
+```bash
+conda activate rna
+
+## salmon Version: salmon 1.1.0
+salmon index -t GRCh38.d1.vd1.CIDC.fa -i salmon_index
+
+...
+index ["salmon_index"] did not previously exist  . . . creating it
+[jLog] [info] building index 
+[jointLog] [info] [Step 1 of 4] : counting k-mers
+[jointLog] [info] Replaced 164,553,847 non-ATCG nucleotides
+[jointLog] [info] Clipped poly-A tails from 0 transcripts
+[jointLog] [info] Building rank-select dictionary and saving to disk
+[jointLog] [info] done
+Elapsed time: 0.191866s
+[jointLog] [info] Writing sequence data to file . . .
+[jointLog] [info] done
+Elapsed time: 1.91244s
+[jointLog] [info] Building 64-bit suffix array (length of generalized text is 3,088,286,426)
+[jointLog] [info] Building suffix array . . .
+success
+saving to disk . . . done
+Elapsed time: 18.3072s
+done
+Elapsed time: 703.843s
+```
+### GMT file for gene set analysis
+
+The GMT file is downloaded from [BROAD release page](https://data.broadinstitute.org/gsea-msigdb/msigdb/release/6.1/). The current GMT file we used is "c2.cp.kegg.v6.1.symbols.gmt"
+
+
+### STAR-Fusion genome resource lib
+
+The genome resource lib is downloaded from [BROAD release page](https://www.gencodegenes.org/human/). The current lib we used is GRCh38_v22_CTAT_lib.
+
+You can also prep it for use with STAR-fusion.
+More details, read:
+
+*  https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion
+
+
+### Centrifuge index
+
+The human Centrifuge index is downloaded from [Centrifuge website](http://www.ccb.jhu.edu/software/centrifuge/). The current index we used is p_compressed+h+v that includes human genome, prokaryotic genomes, and viral genomes.
+
+You can also build your own custom Centrifuge index. 
+More details, read:
+
+*  https://github.com/DaehwanKimLab/centrifuge
+
+### TRUST4 reference files
+
+TRUST4 reference files includes 1. TCR, BCR genomic sequence fasta file; 2. Reference database sequence containing annotation information.
+
+```
+hg38_bcrtcr.fa
+human_IMGT+C.fa
+```
+These reference files can directlt be downloaded from [TRUST4 github](https://github.com/liulab-dfci/TRUST4).
+
+