Question: De-novo transcriptome assembly, annotation and Gene expression profiling using Galaxy Pipeline
gravatar for gouthamsarovaram
7 weeks ago by
gouthamsarovaram0 wrote:

Need Help I'm a PG student doing my dissertation work, it's De-novo assembly, Mapping and Gene expression profiling of entire transcriptome of plants. My source is Illumina HiSeq data from plants. Paired data 1 set control 1 set disease(R1 and R2) for each set. For doing the analysis I have set up a local Galaxy server at the institute and Installed all necessary tools from the Galaxy toolshed to my local instance. My work flow for the analysis so far has been based on assumptions and from the tutorial provided on GitHub and so far the analysis has not been very successful. The following us the Workflow 1) FastQC 2) Trimmomatic 3) FastQC 4) Trinity- Generated two fasta files one for Control and one for Diseased (Did Trinity stat and found out the sequence is good) (So far so good) 5) Deseq2 6) EdgeR 7) Bowtie2 8) Stringtie (From operations 5-8 I have encountered multiple problems one is that I don't have an annotation file and second mainly being that I don't have a reference to run these operations) So I can't map, annotate or check the Gene expressions and the samples I'm using have not been sequence before as well. Would be really helpful if someone could point out the mistakes and help me work up a good workflow.

rna-seq next-gen assembly • 126 views
ADD COMMENTlink written 7 weeks ago by gouthamsarovaram0

You may want to post this question on Galaxy help site to get galaxy specific assistance.

ADD REPLYlink written 7 weeks ago by genomax69k
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