Question: How to visualize a bam file in UCSC Genome Browser
0
gravatar for Azhar
4.6 years ago by
Azhar40
China
Azhar40 wrote:

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 • 5.9k views
ADD COMMENTlink modified 4.5 years ago by Sukhdeep Singh9.9k • written 4.6 years ago by Azhar40
2

Just searching a little bit on google...:

My recommendation is IGV.

ADD REPLYlink written 4.6 years ago by iraun3.6k
2
gravatar for Sukhdeep Singh
4.5 years ago by
Sukhdeep Singh9.9k
Netherlands
Sukhdeep Singh9.9k wrote:

Use bigwig, 

for conversion and visualizations, check
A: Converting Bam To Bedgraph For Viewing On Ucsc?
How Can I Convert Bam/Sam To Wiggle
Visualizing Chip-Seq Data Using Ucsc [Bigwig]

ADD COMMENTlink written 4.5 years ago by Sukhdeep Singh9.9k
0
gravatar for Qi Zhao
4.6 years ago by
Qi Zhao40
China
Qi Zhao40 wrote:

you may try IGV to visualize your data

here is the web link

http://www.broadinstitute.org/igv/

good luck

ADD COMMENTlink written 4.6 years ago by Qi Zhao40

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

ADD REPLYlink written 4.5 years ago by fongchunchan10
0
gravatar for jivarajivaraj
4.6 years ago by
jivarajivaraj50 wrote:

try this link

C: I tried to visualize the bam file in IGV or genome viewer

ADD COMMENTlink written 4.6 years ago by jivarajivaraj50
1

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

ADD REPLYlink written 4.6 years ago by Azhar40

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

ask any question u have please

ADD REPLYlink written 4.6 years ago by jivarajivaraj50
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