[dcjamison]

We align our mRNA-Seq to RefSeq then convert the alignments to bed format, using the UCSC RefSeqAli table as the source for genomic coordinates and splice boundaries. The bed files are saved as bigBed files on our webserver, and distributed back to the researchers as track lines with URLS to paste into the UCSC Browser. We adopted this method because of the rich annotation available in UCSC.

[thinkRNA]

If you search for "sam2bed" in this forum you get this. Hope it helps,
s.

I tried it but doesn't work for me!

[thinkRNA]

UCSC supports BAM format now. So the most direct way is to convert SAM to BAM.

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

[Xi Wang]

Can someone/anyone please recommend a program (that works) to convert SAM formatted data to .bed files that can be viewed in UCSC?

UCSC supports BAM format now. So the most direct way is to convert SAM to BAM.

[steven]

Can someone/anyone please recommend a program (that works) to convert SAM formatted data to .bed files that can be viewed in UCSC?

If you search for "sam2bed" in this forum you get this. Hope it helps,
s.

[thinkRNA]

I've tried IGV, and I use it sometimes, but for me UCSC is still pretty compelling.

1) I like the way the figures it generates look
2) You can see stuff better when you're zoomed way out
3) Easy access to all those nice public data annotation tracks
4) Galaxy/Table browser
5) Non-bioinformatician friendly, easy to send a link that loads custom data
6) I can shove a whole bunch of data in it and go trolling around without having any problems, but for me IGV gets kind of slow. Maybe I'm doing something wrong.

This is probably more of a personal preference kind of situation...

I've tried some of those other ones, IGB, gbrowse, GenomeGraphs, but found them lacking in some way or another.

Can someone/anyone please recommend a program (that works) to convert SAM formatted data to .bed files that can be viewed in UCSC?

[Xi Wang]

1) IGV and IGB are different browsers.
2) GenomeView may be a candidate, but I have not tried.
3) According to the BamView paper, it also works as a plugin for artemis. Artemis loads all kinds of annotation files.

Thanks for pointing out my mistake. I have modified the list, and I will try the last two browsers when I have time.

[lh3]

1) IGV and IGB are different browsers.
2) GenomeView may be a candidate, but I have not tried.
3) According to the BamView paper, it also works as a plugin for artemis. Artemis loads all kinds of annotation files.

[steven]

FYI, I have updated the first post in the thread. I just list some browsers applicable for RNA-seq data viewing. Any suggestion is appreciated in case I lost something important. And also any comment is welcome.

Thanks a lot Xi Wang! If i can this week i will try to complete a bit if possible.

[Xi Wang]

FYI, I have updated the first post in the thread. I just list some browsers applicable for RNA-seq data viewing. Any suggestion is appreciated in case I lost something important. And also any comment is welcome.

[mgogol]

UCSC v IGV

I've tried IGV, and I use it sometimes, but for me UCSC is still pretty compelling.

1) I like the way the figures it generates look
2) You can see stuff better when you're zoomed way out
3) Easy access to all those nice public data annotation tracks
4) Galaxy/Table browser
5) Non-bioinformatician friendly, easy to send a link that loads custom data
6) I can shove a whole bunch of data in it and go trolling around without having any problems, but for me IGV gets kind of slow. Maybe I'm doing something wrong.

This is probably more of a personal preference kind of situation...

I've tried some of those other ones, IGB, gbrowse, GenomeGraphs, but found them lacking in some way or another.

[Xi Wang]

@Xi Wang
You can load to IGV an annotation file on your local computer. The efficiency over network is another issue. Suppose I am sitting in US and want to have a look a huge alignment sitting on a Chinese NFS file server. I can only launch IGV from the Chinese server and then the GUI is transferred over X11 to US. Frequently you will find the responsiveness of the interface is bad due to the limited network bandwidth. A terminal viewer like samtools is much faster. Nonetheless, I guess few people share my this concern.

Yes, we also have this concern. Our group has such project to develop a local browser as well, but still on the way Moreover, the network in China is much poorer, so the local viewer is more needed.

By the way, here is the list of viewers with native support of BAM ("remote" means viewing alignment over HTTP/FTP):

artemis (with bamview plugin)
bamview
gambit
gbrowse (web)
igv (remote)
lookseq (web)
magicviewer
samtools (remote, not supporting annotation)
UCSC browser (web, remote)

Viewers natively supporting BAM are all able to work with huge alignments. The following viewers are able to convert SAM/BAM to their native format. They also work with huge alignment:

gap5
tablet

Great. I just had the idea this afternoon that to list/sort the most important features of these browsers/viewers. Such as supporting SAM. Another feature whether a browser/viewer needs network connection to get annotation tracks is also important.

I am not familiar with the rest, but some certainly have problem with displaying large alignment (e.g. eagleview).

In general, IGV is most matured and easy to use. Samtools may be friendly for some command-line guru, but certainly not useful to RNA-seq as it does not support annotations. You need to do a bit configuration to get lookseq and gbrowse working. But once you set it up, you can host your alignment from your web server and let others have a look. Gambit and magicviewer are under active development. UCSC browser provides another way to host your alignment at UCSC, but I have not tried.

Thank you very much for the info. You are really appreciated.

[Xi Wang]

I'll also quickly add that for some reason known only to our IT department, all our servers will be powered down and offline for this weekend, so anyone trying to download Tablet between now and Monday is out of luck I'm afraid

Yes, I can get to Tablet website hours ago, but can't now :-(

Tablet can read SAM files at the moment, and the version due for release next week will work with BAM too, although it's just an experimental version that parses the file in the same way we handle all formats, so in the short-term you'd still need to read *all* the file. Not good for multi GB files. We will be implementing support for indexed BAM reading though - I think we can manage to make Tablet handle it (and save a ton of memory too) without losing the ability to read all the other formats too.

I like the feature to read SAM/BAM files. It is admitted that SAM is the standard format for sequence/read alignment/mapping, so all browsers/viewers for NGS data should support this format. BAM could be more efficient for large number of reads.

If you have time to add the annotation tracks to Tablet, I am sure that it would have more applications.

Anyhow, thanks for providing your tool!

[imilne]

Viewers natively supporting BAM are all able to work with huge alignments. The following viewers are able to convert SAM/BAM to their native format. They also work with huge alignment:

gap5
tablet

Tablet can read SAM files at the moment, and the version due for release next week will work with BAM too, although it's just an experimental version that parses the file in the same way we handle all formats, so in the short-term you'd still need to read *all* the file. Not good for multi GB files. We will be implementing support for indexed BAM reading though - I think we can manage to make Tablet handle it (and save a ton of memory too) without losing the ability to read all the other formats too.

[lh3]

@Xi Wang

By "inserted sequence" I mean a few bp short insertion. It matters more for SNP calling, but is probably less relevant to RNA-seq.

You can load to IGV an annotation file on your local computer. The efficiency over network is another issue. Suppose I am sitting in US and want to have a look a huge alignment sitting on a Chinese NFS file server. I can only launch IGV from the Chinese server and then the GUI is transferred over X11 to US. Frequently you will find the responsiveness of the interface is bad due to the limited network bandwidth. A terminal viewer like samtools is much faster. Nonetheless, I guess few people share my this concern.

By the way, here is the list of viewers with native support of BAM ("remote" means viewing alignment over HTTP/FTP):

artemis (with bamview plugin)
bamview
gambit
gbrowse (web)
igv (remote)
lookseq (web)
magicviewer
samtools (remote, not supporting annotation)
UCSC browser (web, remote)

Viewers natively supporting BAM are all able to work with huge alignments. The following viewers are able to convert SAM/BAM to their native format. They also work with huge alignment:

gap5
tablet

I am not familiar with the rest, but some certainly have problem with displaying large alignment (e.g. eagleview).

In general, IGV is most matured and easy to use. Samtools may be friendly for some command-line guru, but certainly not useful to RNA-seq as it does not support annotations. You need to do a bit configuration to get lookseq and gbrowse working. But once you set it up, you can host your alignment from your web server and let others have a look. Gambit and magicviewer are under active development. UCSC browser provides another way to host your alignment at UCSC, but I have not tried.