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RNA-Seq: FusionMap: detecting fusion genes from next-generation sequencing data at ba

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  • RNA-Seq: FusionMap: detecting fusion genes from next-generation sequencing data at ba

    Syndicated from PubMed RSS Feeds

    FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.

    Bioinformatics. 2011 May 18;

    Authors: Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W

    MOTIVATION: Next generation sequencing technology generates high-throughput data, which allows us to detect fusion genes at both transcript and genomic levels. To detect fusion genes, the current bioinformatics tools heavily rely on paired-end approaches and overlook the importance of reads that span fusion junctions. Thus there is a need to develop an efficient aligner to detect fusion events by accurate mapping of these junction-spanning single reads, particularly when the read gets longer with the improvement in sequencing technology. RESULTS: We present a novel method, FusionMap, which aligns fusion reads directly to the genome without prior knowledge of potential fusion regions. FusionMap can detect fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution. We showed that FusionMap achieved high sensitivity and specificity in fusion detection on two simulated RNA-Seq datasets which contained 75nt paired-end reads. FusionMap achieved substantially higher sensitivity and specificity than the paired-end approach when the inner distance between read pairs was small. Using FusionMap to characterize fusion genes in K562 chronic myeloid leukemia cell line, we further demonstrated its accuracy in fusion detection in both single-end RNA-Seq and gDNA-Seq datasets. These combined results show that FusionMap provides an accurate and systematic solution to detecting fusion events through junction-spanning reads. AVAILABILITY: FusionMap includes reference indexing, read filtering, fusion alignment and reporting in one package. The software is free for non-commercial use at (http://www.omicsoft.com/fusionmap). CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at the journal's web site.

    PMID: 21593131 [PubMed - as supplied by publisher]



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  • #2
    It suggest that run in 64-bit&6GB. If I selected raw data which is nonmapped read,cloud I ran fusionMap in 32bit&2GB in window?

    Comment


    • #3
      See Q&A session in Fusionmap website:
      http://www.omicsoft.com/fusionmap/#[...it%20mode%3F]]
      Last edited by NGSGE; 05-24-2011, 10:58 AM.

      Comment


      • #4
        Hi,I want to know if fusion junction not follow splice signal(not 2 different gene's exon boundary fuse together), Does FusinMap can detect that fuison-junction?

        Comment


        • #5
          Please see reply in the following page:
          http://omicsoft.com/fusionmap/#[[If%...tect%20it%3F]]

          Comment


          • #6
            Hi,I have a question about FusionMap,In paper,Results,page 4. I don't understand Fig.2,number of false
            and true positives in results using varied parameter combinations.For example,if one spot on (TP,FP)=(20,10),What is the mean of this spot?

            Comment


            • #7
              Please read the "Assessment of fusion detection accuracy" in the supplementary materials on Bioinformatics website.

              Comment


              • #8
                Hi,How many hard drive capacity do I need to prepare,my paired-end data totoal is about 36G. Thanks!

                Comment


                • #9
                  Hi,I don't understand the column of result output,UniqueCuttingPositionCount mean # of distinct reads. What is that mean?

                  I am confused with seed count.

                  Thanks !!

                  Comment


                  • #10
                    FusionMap: Could you please help me for troubleshooting, thank you!

                    Originally posted by Newsbot! View Post
                    Syndicated from PubMed RSS Feeds

                    FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.

                    Bioinformatics. 2011 May 18;

                    Authors: Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W

                    MOTIVATION: Next generation sequencing technology generates high-throughput data, which allows us to detect fusion genes at both transcript and genomic levels. To detect fusion genes, the current bioinformatics tools heavily rely on paired-end approaches and overlook the importance of reads that span fusion junctions. Thus there is a need to develop an efficient aligner to detect fusion events by accurate mapping of these junction-spanning single reads, particularly when the read gets longer with the improvement in sequencing technology. RESULTS: We present a novel method, FusionMap, which aligns fusion reads directly to the genome without prior knowledge of potential fusion regions. FusionMap can detect fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution. We showed that FusionMap achieved high sensitivity and specificity in fusion detection on two simulated RNA-Seq datasets which contained 75nt paired-end reads. FusionMap achieved substantially higher sensitivity and specificity than the paired-end approach when the inner distance between read pairs was small. Using FusionMap to characterize fusion genes in K562 chronic myeloid leukemia cell line, we further demonstrated its accuracy in fusion detection in both single-end RNA-Seq and gDNA-Seq datasets. These combined results show that FusionMap provides an accurate and systematic solution to detecting fusion events through junction-spanning reads. AVAILABILITY: FusionMap includes reference indexing, read filtering, fusion alignment and reporting in one package. The software is free for non-commercial use at (http://www.omicsoft.com/fusionmap). CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at the journal's web site.

                    PMID: 21593131 [PubMed - as supplied by publisher]



                    More...

                    Hi, I tried FusionMap with unmapped fastq data (Illumina Hiseq) on Linux system, the size of input data is about 300Gb, FusionMap worked well for the first 3 days but an error occurred and the program stopped at the 4th day when it preparing the genome search context and generating fusion report. the error notice said segmentation fault. But when I run it with the testdataset, it works well without any problem. Could you please help me for troubleshooting, thank you!

                    Comment


                    • #11
                      FusionMap: trouble, segmentation fault

                      Originally posted by NGSGE View Post
                      See Q&A session in Fusionmap website:
                      http://www.omicsoft.com/fusionmap/#[...it%20mode%3F]]

                      Hi, I tried FusionMap with unmapped fastq data (Illumina Hiseq) on Linux system, the size of input data is about 300Gb, FusionMap worked well for the first 3 days but an error occurred and the program stopped at the 4th day when it preparing the genome search context and generating fusion report. the error notice said segmentation fault. But when I run it with the testdataset, it works well without any problem. Could you please help me for troubleshooting, thank you!

                      Comment


                      • #12
                        I tried with MCF7 PE data set, and the results are not overlapping well with results from TOPHAT-FUSION. Maybe I need to use a better setting?

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