Visualization of BAM files

[Joana Fino]

Hi,

I have been trying to visualize BAM files using the UCSC genome browser.

For what I understand, the genome browser is only capable of display the read alignments in one color, and without orientation.

I was wondering if there is a way to visualize an alignment from a Bam file using some kind of color code, similar to the read visualization on IGV (Integrative genomics viewer - http://software.broadinstitute.org/software/igv/interpreting_insert_size).

 

Thank you for your time,

 

Joana Fino

Bolseira de Investigação

Grupo de Doenças Genómicas | Departamento de Genética Humana

INSTITUTO NACIONAL DE SAÚDE DOUTOR RICARDO JORGE

Avenida Padre Cruz, 1649-016 Lisboa, PORTUGAL

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PENSE ANTES DE IMPRIMIR

 

 

[Luvina Guruvadoo]

Hello Joana,

Thank you for your question. Please have a look at this previously answered question for more information on manually coloring the reads of a BAM file: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/YiGDV5AlkPI/VrnZsIMN7-0J

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.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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[Joana Fino]

Thank you very much for the reply.

I used the YC Tag to color my BAM files, and it worked perfectly!

 

I just have one more question. Besides the color code, is there any way to add the orientation to the visualization? Something similar to the arrows in the BED tracks (https://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr7&hgt.customText=http://genome.ucsc.edu/goldenPath/help/ItemRGBDemo.txt )?

[Matthew Speir]

Hi Joana,

If your BAM alignments are gapless, one of our engineers suggests that you may be able to use the trackDb option "exonArrows on" to display the strand information in your BAM alignment blocks.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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[Joana Fino]

Thank you for the response.

I tried to use the option in gapped and gapless alignments and it didn’t worked.

I was wondering if there is any other suggestion that I could try.

 

Thank you for your help

[Christopher Lee]

Hi Joana,

Unfortunately there is no way to get strand information into the BAM display outside of coloring the reads by strand. However we have noted this as a feature request and we will inform you as soon as it's implemented.

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.

Christopher Lee
UCSC Genomics Institute

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