Hi

[Bhattarai, Sunil]

Hi there,

 

I got this email address from one of the biostar forum I was looking into.

 

I wanted to ask one very basic question. I hope you will help me.

 

I have a sequencing data from the core facility. How do I view that in the ucsc browser and is there a way to extract sequence for each of the transcript.

 

I hope you will direct me to the study material that will be helpful to achieve this.

 

Thank you  

Sunil

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[Brian Lee]

Dear Sunil,

Thank you for using the UCSC Genome Browser and your question about taking sequencing data from your core facility to a step where you can extract sequence for each transcript.

Your question is at a high-level, could you share what kind of data you have? Some core facilities help with processing sequence data, are you at that state? If you are looking to identify transcripts from within raw sequence information it is likely beyond the scope of our mailing list and searching the wider network of bioinformatic resources like Biostars and Seqanswers would likely better serve you where you might be pointed to other resources like g-onramp (http://gonramp.wustl.edu/?page_id=384) that provide virtual box machines you can locally install to process fasta and rna-seq data into assembly browsers (but again this is beyond the scope of our list).

On the other hand if you have BAM files, you can view those as custom tracks when hosted at an internet accessible location like CyVerse for free (although if you have very confidential patient data, you may wish to use our Virtual Machine called the GBiB http://genome.ucsc.edu/goldenpath/help/gbib.html to do all your data viewing locally). However, as stated in the last paragraph, if you have unaligned sequence reads, you'll probably need to search out community help beyond our list.

In the mean time, if you want to learn more about our tools we have a training page with video links http://genome.ucsc.edu/training/index.html and we have an archived mailing list you can search https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome where you can often get more in-depth information we can't always fit into every email response.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genomics Institute

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