Question_and_Answer

Questions and Answers

1. Is SOAPfuse able to analyze RNA-Seq of other organism?

   
   So far, SOAPfuse is developed only for analysis on RNA-Seq data of tissues from human being. But, you can implement the method on the RNA-Seq data from other organism to seek fusions.
   
   

2. What's the difference between SOAPfusion and SOAPfuse in BGI website?

   
   SOAPfuse and SOAPfusion are totally different with each other. They are based on different algorithms. Although they are both developed by BGI and their names are similar, they are developed by different teams of BGI.
   
   

3. Can I use SOAPfuse to analyse the Exome-Seq data?

   
   SOAPfuse use two types of reads (called span-read and junc-read) to support fusion detection. Both of this two types require the PE-sequenced segment covers the fusion junction point. As we know, the classical fusion genes, that have been reported in lots of fusion-studies, are derived from the chromosome rearrangements (or structure variations, SV) on genome. The breakpoints of SV always locate at the intron or the intergenic region. It is easy to understand that the fusion transcript sequence we detected is transcribed from the SV mutated region, and after the splicing on pre-mRNA. We can consider the Genome sequenced segments are from the pre-mRNA, including unspliced intron. So genome-Seq data is not suitable to detect fusion using SOAPfuse. Moreover, the Exome-Seq is a regional sequencing strategy, and the probes it uses make one segment unlikely to cover two or more exons. So, Exome-Seq is also unsuitable to operate SV detection based on cluster method. Of course, other methods maybe ok, such as that based on differential covered depth of exons.
   If you have Genome-Seq data, including Exome-Seq, we suggest you to use these data to detect the SVs that generate the fusion genes.
   
   

4. The format of original RNA-Seq reads

   
   Click here to know about the standard format SOAPfuse is developed to recognize.
   Click here to know the pre-treatment on RNA-Seq read-id operated by SOAPfuse.
   
   

5. What's the function of TEMP directory and the '-tp' parameter?

   
   As we know, all software and tools generate temp files. SOAPfuse also has its temp files. It creates the TEMP directory in the OUTDIR provided by user. In the TEMP directory, sub-directory is also created. The sub-directory is named as 'config_shell.xxx', where 'xxx' is as same as the value you set to '-tp' parameter. So, if you have more than one samples that need to run SOAPfuse in parallel, as long as you set the '-tp' as the sample-ID, the temp dir of each run (for each sample) can be easily distinguished. You may click here to know about the '-tp' parameter.
   In the TEMP directory, you can find the shell scripts and log files corresponding to all steps (from s01 to s09). Of course, they are generated step by step. The shell script contains all shell commands (in linux OS), you can read it to know all operations of SOAPfuse pipeline. And, the log file contains the realtime log-output of the running step. Once the running step finishes successfully, the log file will be replaced by the alert of success or failure, and all its log-out content will be moved to the STDERR of SOAPfuse. Of course, if SOAPfuse fails at one step, the corresponding log file will be greatly helpful to find the reason and debug the SOAPfuse.
   
   

6. Is the content in SourceForge/SOAPfuse different from that on its SOAP official website?

   
   The official website of SOAPfuse is still on the BGI-SOAP-homepage. BGI-SOAP-homopage is maintained by other persons (I cannot modify in good time), and it is hard to set up multiple-web-page (topological structure) on the BGI-SOAP-homopage. From v1.26, I copied the official website to the SourceForge/SOAPfuse Project wiki-page with some updates. On SourceForge, it is easy to post blogs, and add new pages. Of course, I will try my best to make the official website synchronized with SourceForge/SOAPfuse Project content.
   
   

7. SOAPfuse fails at the step s08, reporting wrong start_codon

   
   It has been fixed in v1.27. Please check link below.
   Check the step-log in TEMP/config_shell.xxx/fusion.s08.singlefork/fusion.s08.sh.log,
   it may report an error: wrong start_codon.
   This may be caused by the base-number error of start_codon, pls click here to know about it.
   And, may be caused by the sequence error of start_codon, pls click here to know about it.
   
   

8. Gene_names or transcript_names with postfix string like "SOAPfuse2SOAPfuse"

   
   New naming strategy has been applied in v1.27. Please check link below.
   This is because the repeated gene_names and transcript_names in the GTF file, click here to know about it.
   
   

9. Do I need step s09?

   
   Step s09 is only for further analysis of fusion genes. Click here to know about it.