Hey,
Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next
gen transcriptome data setthat I would like to align and quantify against a
list of expected transcripts from Mimulus guttatus. The expected transcripts
are in .gff format, and I was wondering how I could get
Hello,
To use a custom genome with the alignment tools at Galaxy Main
(http://usegalaxy.org), the dataset must be in fasta format. If the data
is RNA, then using the tools in NGS: RNA Analysis will accept both a
reference custom genome and a transcript file in GTF format to guide
placement
Also, I'm working under John Kelly and Lena Hileman at KU. We, along with our
collaborators at Duke, would get a lot of use out of an expected transcriptome
that we could blast illumine data against. If we sent you our genome in .fasta
format along with the .gff expected transcript file is
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