[Xi Wang]

Xi Wang, Thanks for your suggestion. Whats a good program to convert SAM to BAM? I am using bowtie to get SAM formatted data. Thanks so much!

priyam

See samtools:

http://samtools.sourceforge.net/

After you install samtools, use the scrpt:

samtools import <in.ref_list> <in.sam> <out.bam>

where <in.ref_list> is a TAB-delimited file: Each line must contain the reference name and the length of the reference, one line for each distinct reference; additional fields are ignored. This file also defines the order of the reference sequences in sorting.
<in.sam> is the SAM file input, and <out.bam> is the BAM file output.

[dcjamison]

I align my RNA-Seq to mm9 and want to view my reads on UCSC. I am planning on using bigBed file on my webserver just as you describe. I am just lost why would you need the RefSeqAli table?

We are interested in alternative splicing and reads which bridge exons. Since we align to RefSeq, we use the RefSeqAli file to convert from RefSeq to genomic coordinates. If you've aligned to the genomic coordinates, you don't need to convert the coordinates, but you have lost the reads which cross splice boundaries.

[Thomas Doktor]

You should try TopHat as well, which can align reads spanning exon-exon junctions using a standard genomic reference. You can supply your own junctions or a reference GFF file, but TopHat is also able to identify previously unreported splice junctions.

[dcjamison]

We looked at it when it first came out, and it would have involved making too many changes in our data workflow for too little benefit -- lots and lots of scripts to change

As things are simplifying with the new Illumina softwares, we might take a look at it again.

[Nix]

Igb

I use IGB extensively for RNA-Seq visualizations, both paired and single reads, read coverage graphs, and for window enrichment analysis. It's quite exceptional and has parsers for most of the commonly used file formats. The folks at UNC at Charlotte http://igb.bioviz.org/ are really pushing the code base. They are building in support for BAM and SAM. (I should say that there are some major problems with using SAM and BAM for RNA-Seq data, see my posts in http://seqanswers.com/forums/showpos...3&postcount=28 )

I convert most everything to useq bed12 format and use GenoPub to annotate, organize, and distribute my genomic datasets. See http://bioserver.hci.utah.edu/BioInf.../Software:DAS2 for details.

P.S. IGB was around many years before IGV. Not sure why the folks at the Broad decided to copy it's name.

[Jim Robinson]

I am the "folks at Broad" so I guess I should respond re the name. I did not copy it, I was actually not aware of IGB. If I had been I assure you another name would have been chosen, it causes much confusion. IGV began its life as a visualizer of aCGH data, and our model was dChip, it grew from there to do other things. I'm not trying to "catch up on functionality", IGV development is driven primarily by internal needs at the Broad.

[Nix]

OK. It's good to have all of these choices in visualizations. Lots of cross pollination. I know the GenoViz folks (I'm one too but don't work on IGB directly) are looking at how you've implemented the bp visualization of stacked reads.

[Jim Robinson]

Yes, choices are good for everyone. I've learned about IGB recently of course, its very full featured. IGV's focus is different, its a simpler browser with an emphasis on handling big files. There is some overlap of course. Again, the name is very unfortunate, that's my bad.

[Xi Wang]

A review summarizes sequence viewers and genome browsers

Hi guys,

Please see attached.
This paper gives a comprehensive summarization.

[Dongliang Ge]

You may also want to check this out:

http://www.svaproject.org/

We develop SequenceVariantAnalyzer, or SVA, trying to annotate and visualize SNP, INDEL, and larger SVs, with an integrated genome browser:



More screenshots here:

http://www.svaproject.org/screenshots.php

I need to point out that SVA is designed to annotate and visualize the variants called, but not the short reads.

[ohomann]

I saw my software, MochiView, on the list of programs for visualizing RNA-Seq data, and thought I'd engage in a bit of self-promotion (because, after all that work, I don't want it to be one of the hundreds of informatics programs that die the grisly death of obscurity ).

I recently published a paper about the software, and the website contains a lot of additional information, including a feature list and demo videos. MochiView doesn't cover exactly the same ground as all the other excellent programs in your compiled list, but it does excel in the data visualization and browsing department.

I'm still actively working on the software, and I always welcome questions and suggestions!

[Xi Wang]

I saw my software, MochiView, on the list of programs for visualizing RNA-Seq data, and thought I'd engage in a bit of self-promotion (because, after all that work, I don't want it to be one of the hundreds of informatics programs that die the grisly death of obscurity ).

I recently published a paper about the software, and the website contains a lot of additional information, including a feature list and demo videos. MochiView doesn't cover exactly the same ground as all the other excellent programs in your compiled list, but it does excel in the data visualization and browsing department.

I'm still actively working on the software, and I always welcome questions and suggestions!

Thank you very much for providing us this wonderful tool, and letting us know the information.

[aloraine]

IGB is Integrated Genome Browser and it supports display of RNA-Seq data from BAM files, the feature people reading this forum would probably be most interested in. It can also display annotations in BED format, alignments from blat (PSL), tiling array data, and many other data types. A major difference between it and other genome browsers is that it implements animated zooming, which means the zooming happens dynamically as you operate the zoom sliders. It is highly-configurable - many people use it to make high-quality images for publication. You can change the relative position of tracks, merge minus and plus strand tracks or split them apart, change forground and background colors, change the labels that appear on tracks and above annotations, and so on. It also lets you view data from lots of different genomes via its connections to various Distributed Annotation servers, including the DAS1 server at UCSC. So..if you can see it in the UCSC Genome Browser, then you can also view it in IGB! But IGB also supports visualization of other genomes not supported at UCSC, including many plant genomes, Dicty, E coli, and others. For more information, visit http://www.bioviz.org/igb.

[Xi Wang]

IGB is Integrated Genome Browser and it supports display of RNA-Seq data from BAM files, the feature people reading this forum would probably be most interested in. It can also display annotations in BED format, alignments from blat (PSL), tiling array data, and many other data types. A major difference between it and other genome browsers is that it implements animated zooming, which means the zooming happens dynamically as you operate the zoom sliders. It is highly-configurable - many people use it to make high-quality images for publication. You can change the relative position of tracks, merge minus and plus strand tracks or split them apart, change forground and background colors, change the labels that appear on tracks and above annotations, and so on. It also lets you view data from lots of different genomes via its connections to various Distributed Annotation servers, including the DAS1 server at UCSC. So..if you can see it in the UCSC Genome Browser, then you can also view it in IGB! But IGB also supports visualization of other genomes not supported at UCSC, including many plant genomes, Dicty, E coli, and others. For more information, visit http://www.bioviz.org/igb.

Thank you for the great improvement! It's really quite useful in RNA-seq and other researches. I will update the first post in this thread.