How to read modEncode RNA-seq data?

Kaveh · 10-06-2010, 01:43 PM

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

malachig · 10-06-2010, 09:56 PM

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!

steven · 10-07-2010, 07:00 AM

Quote:

Originally Posted by malachig

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!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
RNA SEQ Data read counts from known and unknown regions	deveci	Bioinformatics	0	06-24-2011 03:33 PM
RNA-Seq: Querying large read collections in main memory: a versatile data structure.	Newsbot!	Literature Watch	0	06-21-2011 03:00 AM
RNA-Seq: X-MATE: A flexible system for mapping short read data.	Newsbot!	Literature Watch	0	01-11-2011 08:20 AM
RNA-Seq: Modeling non-uniformity in short-read rates in RNA-Seq data.	Newsbot!	Literature Watch	2	06-29-2010 02:47 PM
RNA-seq data with read of >= 50-bp length	Xi Wang	Bioinformatics	0	01-15-2010 01:01 AM

10-06-2010, 01:43 PM	#1
Kaveh Junior Member Location: USA Join Date: Oct 2010 Posts: 2	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

10-06-2010, 09:56 PM	#2
malachig Senior Member Location: WashU Join Date: Aug 2010 Posts: 117	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!