Question

How to visualize a bam file in UCSC Genome Browser

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9.6 years ago

Azhar ▴ 50

I have a 1.31 GB bam file, is it too big to view in ucsc browser, if it is then what is the alternate solutions

ChIP-Seq • 10k views

ADD COMMENT • link updated 21 months ago by Ram 44k • written 9.6 years ago by Azhar ▴ 50

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Just searching a little bit on google...:

My recommendation is IGV.

ADD REPLY • link updated 22 months ago by Ram 44k • written 9.6 years ago by iraun 6.2k

Ram · Answer 1 · 2015-05-29

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9.5 years ago

Sukhi Singh 11k

Use bigwig, for conversion and visualizations, check

ADD COMMENT • link updated 22 months ago by Ram 44k • written 9.5 years ago by Sukhi Singh 11k

Ram · Answer 2 · 2015-05-08

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9.6 years ago

Qi Zhao ▴ 50

You may try IGV to visualize your data. Here is the web link: http://www.broadinstitute.org/igv/

Good luck

ADD COMMENT • link updated 22 months ago by Ram 44k • written 9.6 years ago by Qi Zhao ▴ 50

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You can also download the data tracks from UCSC and add it IGV.

ADD REPLY • link 9.5 years ago by fongchunchan ▴ 10

Ram · Answer 3 · 2015-05-08

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9.6 years ago

jivarajivaraj ▴ 50

ADD COMMENT • link updated 22 months ago by Ram 44k • written 9.6 years ago by jivarajivaraj ▴ 50

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How to install IGV veiwer cz it is jnlp file not exe.

ADD REPLY • link updated 22 months ago by Ram 44k • written 9.5 years ago by Azhar ▴ 50

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Download IGV_2.3.23.zip from this link: http://www.broadinstitute.org/software/igv/download then unzip it in unzipped file you can find an icon as igv.jar. Click to install.

Ask any question you have please

ADD REPLY • link updated 22 months ago by Ram 44k • written 9.5 years ago by jivarajivaraj ▴ 50