Tutorial¶
The follow tutorial explains how to execute ChimPipe to identify already known fusion genes on the MCF-7 Breast cancer cell line.
A total of 6 different fusion genes have been experimentally validated by Edgren et al. (Genome Biology, 2011) and Kangaspeska et al. (PLOSone, 2012). 5 of them are detected by ChimPipe:
| Fusion Gene | Chimeric splice-junctions | Detected |
|---|---|---|
| BCAS4-BCAS3 | chr20_49411710_+:chr17_59445688_+ | Yes |
| ARFGEF2-SULF2 | chr20_47538547_+:chr20_46365686_- | Yes |
| RPS6KB1-VMP1 | chr17_57992064_+:chr17_57917129_+ | Yes |
| GCN1L1-MSI1 | chr12_120628101_-:chr12_120785317_- | No |
| AC099850.1-VMP1 | chr17_57184952_+:chr17_57915656_+ | Yes |
| SMARCA4-CARM1 | chr19_11097269_+:chr19_11015627_+ | Yes |
1. Download ChimPipe¶
Check our Installation section for details about how to download and install ChimPipe.
2. Download all-in-one package¶
This package contains all the needed files for executing ChimPipe on MCF-7 RNA-seq data in the “input” folder:
- Paired-end RNA-seq data: MCF-7_1.fastq.gz and MCF-7_2.fastq.gz
- Gencode 19 annotation: gencode.v19.annotation.long.gtf
- Genome index: Homo_sapiens.GRCh37.chromosomes.chr.M.gem
- Transcriptome index: gencode.v19.annotation.long.gtf.junctions.gem
- Transcriptome keys: gencode.v19.annotation.long.gtf.junctions.keys
- Similarity matrix: gencode.v19.annotation.long.similarity.txt
Click here to download.
3. Execute ChimPipe on MCF-7¶
ChimPipe.sh --fastq_1 MCF-7_1.fastq.gz --fastq_2 MCF-7_2.fastq.gz
-g Homo_sapiens.GRCh37.chromosomes.chr.M.gem -a gencode.v19.annotation.long.gtf
-t gencode.v19.annotation.long.gtf.junctions.gem -k gencode.v19.annotation.long.gtf.junctions.keys
--sample-id MCF-7 --threads 4 --similarity-gene-pairs gencode.v19.annotation.long.similarity.txt
4. Examine your output¶
ChimPipe identifies 13 chimeric transcript, including 5/6 validated cases and 3 readthrough transcripts.
We provide ChimPipe output for MCF-7 on the “output” folder. If everything is ok, your results should be identical as the ones provided.
Check our Manual section for an explanation about ChimPipe output files.