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Old 10-06-2010, 01:43 PM   #1
Kaveh
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Default How to read modEncode RNA-seq data?

When I download the RNA-seq data of my desired gene for certain stages of drosophila embryo, modEncode gives me a ".sam" file. I open it with MS excel but columns don't have a label.

I am generally asking for some resources to become familiar with reading the data, and specifically want to know how to sort that type of tables and figure out the abundance of my gene in different stages.

thanks for your inputs
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Old 10-06-2010, 09:56 PM   #2
malachig
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The kinds of files you are going to encounter in the area of RNA-seq analysis will generally not be something that can be adequately visualized or manipulated in excel. There are various viewers available that are specifically designed to deal with SAM files. For example, this forum has an excellent posting on the topic:
Browsers/Viewers for RNAseq .

Other tools allow you to extract information of various types from SAM files. If you search this forum you will find many discussions relevant to examining RNA-seq data for a series of comparisons. Some links that come to mind are:
DEGseq, DEseq, Myrna, Guide/tutorial for RNA-seq analysis, quantifying transcript levels using RNA-seq, edgeR, etc.

Search the forums, post specific questions that haven't been covered yet, and good luck!
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Old 10-07-2010, 07:00 AM   #3
steven
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Quote:
Originally Posted by malachig View Post
The kinds of files you are going to encounter in the area of RNA-seq analysis will generally not be something that can be adequately visualized or manipulated in excel.
One of the best answers i have seen in this forum
I couldn't put it better.

But hey, maybe one day this will change! Have you guys heard about Bioxcel, from the Microsoft Biology Initiative? They are developing some funny bioinfo toolkit including pairwise alignment algorithms and operations on genomic intervals, all in excel. Bedtools, biopieces, galaxy et al., beware!
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