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Old 03-19-2010, 09:35 AM   #1
Location: New York

Join Date: Dec 2009
Posts: 42
Default Igv

Greetings All,
I have been using IGV to view my bowtie alignments in BAM format but am experiencing some difficulty. I have to drill down to the last 2 levels of sequence magnification to actually see where my alignments match up against my reference. Does anyone else have this issue? Additionally, is there a away that I can format these so I do not have to drill down so far, thus allowing me to look at a more global picture of the RefSeq genes? any help is appreciated.

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Old 03-19-2010, 10:14 AM   #2
Thomas Doktor
Senior Member
Location: University of Southern Denmark (SDU), Denmark

Join Date: Apr 2009
Posts: 105

You need to make a coverage profile using the "igvtools count" command, this will create a lightweight coverage profile which can be seen on a global scale.

The command would be something like:
igvtools count alignment.bam alignment.bam.tdf hg19

Read more here:
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Old 03-19-2010, 10:46 AM   #3
Location: New York

Join Date: Dec 2009
Posts: 42

@Thomas Doktor,
Thanks for the info but everytime I attempt to run the igvtools count command it tells me it cannot find the genome file, regardless if I give it the name "hg19" or the full path. any ideas?
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Old 06-04-2010, 07:19 PM   #4
Jim Robinson
Location: Boston, MA

Join Date: May 2009
Posts: 75

Hi, if you're still having troubles with this email

You can increase the window size for which alignments are displayed from the user preferences, click "View > Preferences > Alignments (tab)" and change the "Visibility Range Threshold". Its set for 30kb, which is a reasonable default, but if your coverage is not excessively deep you can increase it safely.

I don't know why you are getting the error with igvtools, again if you're still experiencing this please email.

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