Dear galaxy users,

     I aligned my RNA-seq data by using Tophat in galaxy. It generated some  “Tophat deletions”, “Tophat insertions” and “Tophat splice junctions” results. These are all BED files. Does anyone know how to use/analyze these kind of results?

     Also, I used illumina RNA-seq. Each biological sample has 36-48 million reads. The data for each sample were divided to 10-12 FASTQ files. When I did the “FASTQ Summary Statistics” and draw “boxplot” for each of the sub-file, the score value is about 9-10. Is it too low? Shall I combine the FASTQ files for each biological sample and do the statistics again?

     At last, does anyone know how to convert a long list of zebrafish genes (500-1000 genes) to human or mammalian orthologs?

Thank you for your replies,

         Xiefan Fang

University of Florida