Question

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

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10.0 years ago

jivarajivaraj ▴ 50

hello guys

please someone help me again

i have indexed sorted.bam file and want to visualize it in IGV or genome viewer in windows

i launched or downloaded bamview but it says application cant be launched, my java is 32

what can i do to visualization????

next-gen • 4.5k views

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by jivarajivaraj ▴ 50

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What specific error message is it giving you?

Alternatively, you can upload it to Galaxy and view it there.

ADD REPLY • link 10.0 years ago by Dan D 7.4k

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Hello Dan

What I exactly want to do is indexed sorted.bam file visualization by IGV or genome browser.

I did these steps: I downloaded IGV and produced indexed sorted.bam file. For visualization, whether I need to use BamView or I can upload my file directly to IGV? I downloaded BamView but when launching it said: application cant be launched

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by jivarajivaraj ▴ 50

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IGV wants your indexed BAM file. You mentioned that IGV wouldn't launch. It should have given you a specific error message. If you can tell me what that message said, I may be able to help you start IGV on your machine. Sometimes IGV needs some love before it will run properly.

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by Dan D 7.4k

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Thank you Dan - at last I launched bamview

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by jivarajivaraj ▴ 50

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Hello Dan

I have two fastq files, first set are the footprints, while the second sets are data coming from a common RNA-seq experiment performed in parallel, I want to adapter sequences, using the software CUTADAPT

The adapter sequences are:

GTTCAGAGTTCTACAGTCCGACGATC # 5 prime adapter sequence
ATCTCGTATGCCGTCTTCTGCTTG # 3 prime adapter sequence

May you please tell whether and how I can do this project with windows seven 64 bit?

Help me please

Thank you

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 9.6 years ago by jivarajivaraj ▴ 50

score 1 · Answer 1 · 2014-12-10

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10.0 years ago

GouthamAtla 12k

Download IGV. index your bam file and reference genome. Load reference genome first ( genome --> load geome). Then load bam file (file --> load file). Go to the chromosome of your interest and zoom.

If your computer does not have good configuration, get subset of reads from bam file (may be chromosome wise) and load them.