Hello everyone!
I am here collecting the information of browsers/viewers especially for RNA sequencing data, which can mainly show the gene annotation track, read track (including spliced reads), and some other annotation tracks. This is the basic requirment of RNA-seq data viewing.
Thanks to the Seqanswers wiki page, I listed the browsers/viewers for RNA-seq below. But due to my limited experience, the list is not full. Anyone helps to complete this list is appreciated. Also, the unique feature for each browser/viewer is important, as users can choose their own browser/viewer accordingly. Could please help me to fill them too?
Thanks in advance for your time and your attention!
EDIT: I have collected some browsers applicable for RNA-seq. It seems too few due to the requirement of gene annotation tracks.
I am here collecting the information of browsers/viewers especially for RNA sequencing data, which can mainly show the gene annotation track, read track (including spliced reads), and some other annotation tracks. This is the basic requirment of RNA-seq data viewing.
Thanks to the Seqanswers wiki page, I listed the browsers/viewers for RNA-seq below. But due to my limited experience, the list is not full. Anyone helps to complete this list is appreciated. Also, the unique feature for each browser/viewer is important, as users can choose their own browser/viewer accordingly. Could please help me to fill them too?
Code:
Lookseq MochiView SeqMonk IGV MagicViewer SAMtools UCSC genome browser GenomeGraphs
EDIT: I have collected some browsers applicable for RNA-seq. It seems too few due to the requirement of gene annotation tracks.
Code:
Software Author Affiliation Supported_format Remote Unique_feature Link IGV Broad Institute TDF,CN,SNP,GCT,RES,GFF/GFF3,BED,SAM/BAM,WIG,TAB,IGV... Yes supports a wide variety of data types and format http://www.broadinstitute.org/igv/ IGB UNC Charlotte BAM,BED,PSL,... animated zooming, highly configurable,.. http://www.bioviz.org/igb UCSC Browser UCSC BED,bigBed,BEDGRAPH,GFF,GTF,WIG,bigWig,MAF,BAM,PSL Yes various of annotation tracks, Working with table browser http://genome.ucsc.edu/ CisGenome Browser Stanford BAR,BED,refFlat,FA,... fold intron, show UCSC tracks http://biogibbs.stanford.edu/~jiangh/browser/ MochiView UCSF Wig,Bed,GFF,FASTA,MEME joint analysis of ChIP-seq and RNA-seq data http://johnsonlab.ucsf.edu/sj/mochiview-start/ SeqMonk The Babraham Institute ELAND,GFF,BED,MAQ,SAM nice plot, data filter http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/ Gambit Boston College BAM,BED,GFF2,GFF3,FASTA,VCF plugin-aware http://code.google.com/p/gambit-viewer/ GenomeGraphs Lawrence Berkeley Expression data,Annotation tracks Bioconductor package http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html GenomeView BamView+artemis "Remote" means viewing alignment over HTTP/FTP
Comment