目录

Fusioncatcher

http://39.106.215.109/dokuwiki2/doku.php?id=售后:针对医口人融合基因分析&do=edit

软件功能

软件功能： 针对人的融合基因的分析的功能软件。

软件特点

FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

The aims of FusionCatcher are:

  1. very good detection rate for finding candidate fusion genes,
  2. very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher),
  3. very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc.
  4. to be as automatic as possible (i.e. the FusionCatcher will choose automatically the best parameters in order to find candidate fusion genes, e.g. finding automatically the adapters, building the exon-exon junctions automatically based on the length of the input reads, etc.) while providing the best possible detection rate for finding fusion genes.

使用方式

/TJPROJ6/RNA_SH/software/fusioncatcher/fusioncatcher-master/bin/fusioncatcher -i work_dir -o out_dir

结果解读

The output files:

1. final-list_candidate_fusion_genes.txt ###### 

  final list with the newly found candidates fusion genes (it contains the fusion genes with their junction sequence and points); Starting with version 0.99.3c the coordinates of fusion genes are given here for human genome using only assembly hg38/GRCh38

2. final-list_candidate_fusion_genes.caption.md.txt ####### 

  explains in detail the labels found in column Fusion_description of files final-list_candidate_fusion_genes.txt

3. supporting-reads_gene-fusions_BOWTIE.zip ####### 

  sequences of short reads supporting the newly found candidate fusion genes found using only and exclusively the Bowtie aligner;

4. supporting-reads_gene-fusions_BLAT.zip ####### 

  sequences of short reads supporting the newly found candidate fusion genes found using Bowtie and Blat aligners;

5. supporting-reads_gene-fusions_STAR.zip ####### 

  sequences of short reads supporting the newly found candidate fusion genes found using Bowtie and STAR aligners;

6. supporting-reads_gene-fusions_BOWTIE2.zip ####### 

  sequences of short reads supporting the newly found candidate fusion genes found using Bowtie and Bowtie2 aligners;

7. viruses_bacteria_phages.txt ####### 

  (non-zero) reads counts for each virus/bacteria/phage from NCBI database ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/