![]() ![]() These files come with starchip for human hg19 and hg38 in the reference directory. Starchip-fusions can also make use of known antibody parts, and copy number variants. The files needed are already included in the directory of STARChip. If you’re working on hg19 or hg38, you don’t have to do the following things. On your local machine sort the bed file: sort -k1,1 -k2,2n repeats.bed >.Click ‘get output’ to download your bed file.Following the instructions in the picture to download repeats from UCSC genome browser. Starchip-fusions filters using the location of known repeats in bed format as well. setup.sh ~/RefData/Homo_sapiens/GENCODE_v27/ ~/RefData/Homo_sapiens/GRCh38_no_alt/genome.fa. STARChip makes use of gtf files for annotating fusions and circRNA with gene names.įirst, download the package and prepare annotation files: 1 STAR -genomeDir /path/to/starIndex/ -readFilesIn file1_1.fastq.gz file1_2.fastq.gz -runThreadN 11 -outReadsUnmapped Fastx -quantMode GeneCounts -chimSegmentMin 15 -chimJunctionOverhangMin 15 -outSAMstrandField intronMotif -readFilesCommand zcat -outSAMtype BAM Unsorted reference/BED files Your project will have it’s own requirements, but a good starting point for your star alignments might look like: Run STAR with the following parameters required for chimeric output: –chimSegmentMin X –chimJunctionOverhangMin X (where X is an integer). Not doing so will strongly inflate your false positives rate, because reads that map perfectly to an unplaced contig will instead find the next best alignment, often a chimeric alignment. It is absolutely critical however, that you follow the STAR manual’s instructions and build a genome using all chromosomes plus unplaced contigs. ![]() See the STAR documentation for installation, as well as building or downloading a STAR genome index. In most instances to run STARChip you must first run star on each of your samples. It is optional for STARChip to run STAR on your samples. STARChip is written to be an extension of the STAR read aligner. Notes below are more for my own convenience.
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