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

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