User: puvan001@umn.edu

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Posts by puvan001@umn.edu

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Comment: C: Rna Seq Analysis
... Hi Thank you! yes, your guess is correct. Now it works. Sumathy It sounds like you're on the right track. To visualize data for a custom build in Trackster, you need to create a custom build and use that in Trackster: Important note: you'll need to make sure that your contig name match ...
written 7.1 years ago by puvan001@umn.edu80
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Comment: C: Rna Seq Analysis
... Hi Thanks! I am little bit familiar with IGV. I'll try then. Sumathy One of the problem is IGV dont have option of creating index file so one has to create index file in Galaxy first to  view in IGV. Jim I have been using IGV 2 beta version it is great work but How hard is to include index ...
written 7.1 years ago by puvan001@umn.edu80
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Comment: C: Rna Seq Analysis
... Hi I may be doing in a wrong way. I clicked trackster and I added the custom build genome. Since it is a very small genome (~2kb), I considered this as a single contig. Then I cliked "add tracks" and added my data file. But I got a message "no data for this contig. Whenever I used built in genome ...
written 7.1 years ago by puvan001@umn.edu80
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Comment: C: Rna Seq Analysis
... Hello I was able to run RNA seq data against a custom build genome. How can I visualize the results. I tried via trackster and unfortunately I couldn't. Can you help me? Thanks Sumathy ...
written 7.1 years ago by puvan001@umn.edu80
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Comment: C: Rna Seq Analysis
... Hi Austin I did all these (grooming and trimming)on rna-seq data and I don't have a problem with built in genome . I'll try again! Thanks Sumathy it says "History does not include a dataset of the required format / build". for you when tophat is called. Secondly you should leave the ...
written 7.1 years ago by puvan001@umn.edu80
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Comment: C: Rna Seq Analysis
... Hi David, Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and it says "History does not include a dataset of the required format / build". Do you have any thoughts about this? Now it makes more sense about "multihits". Thanks for sharing your workflow. With regards Sumathy ...
written 7.1 years ago by puvan001@umn.edu80
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Rna Seq Analysis
... Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind ...
galaxy written 7.1 years ago by puvan001@umn.edu80 • updated 7.1 years ago by David Matthews630
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Rna Seq Analysis
... I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the steps up to cufflinks and I did not have any problems. Thanks for the RNA seq tutorial. My questions are 1. How do I know the number of reads mapped against the reference genome used after Top Hat mappin ...
cufflinks rna-seq written 7.2 years ago by puvan001@umn.edu80 • updated 7.1 years ago by Jennifer Hillman Jackson25k

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