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========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:
    - very good detection rate for finding candidate fusion genes,
    - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher),
    - very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc.
    - 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/

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