Forum: Bioinformatics
11-01-2015, 02:56 PM
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Replies: 16
Views: 4,162
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Forum: Bioinformatics
11-01-2015, 08:04 AM
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Replies: 16
Views: 4,162
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Forum: Bioinformatics
11-01-2015, 01:48 AM
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Replies: 16
Views: 4,162
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Forum: Bioinformatics
11-01-2015, 01:14 AM
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Replies: 16
Views: 4,162
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Forum: General
06-17-2013, 07:04 AM
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Replies: 4
Views: 7,888
Hi,
This is not something IGV currently...
Hi,
This is not something IGV currently does. As you can see from my last post I'm not clear on the specifics of how a consensus sequence is defined, other than as a pileup. Some decision needs...
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Forum: Bioinformatics
02-03-2013, 04:33 AM
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Replies: 8
Views: 3,400
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Forum: Bioinformatics
01-16-2013, 06:20 AM
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Replies: 11
Views: 14,711
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Forum: Bioinformatics
12-12-2012, 08:41 AM
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Replies: 4
Views: 2,119
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Forum: Bioinformatics
12-12-2012, 06:54 AM
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Replies: 4
Views: 2,119
Hi,
What version of IGV are you using? It...
Hi,
What version of IGV are you using? It should automatically recognize and alias identifiers of that sort.
I'm sure there are more direct ways to do this, but this method works. First cut...
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Forum: Bioinformatics
11-24-2012, 06:23 PM
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Replies: 11
Views: 14,711
I'm pretty late to this thread, missed the...
I'm pretty late to this thread, missed the original post. However, for the record IGV displays blat output in the form of .psl files, the extension must be .psl. There's no need to convert it to...
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Forum: Bioinformatics
09-26-2012, 07:29 AM
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Replies: 7
Views: 2,228
Hi,
Could you contact us at...
Hi,
Could you contact us at igv-team@broadinstitute.org? We can arrange to maybe transfer your reference genome and a test file.
Also, the new early access version of IGV should not return...
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Forum: Bioinformatics
09-25-2012, 03:54 AM
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Replies: 7
Views: 2,228
Hi, this looks like an IGV bug (obviously). I...
Hi, this looks like an IGV bug (obviously). I am trying to reproduce it, in the meantime could you try the "early access" version to see if the bug is fixed there, if not please send or post the...
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Forum: Bioinformatics
09-11-2012, 05:29 AM
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Replies: 1
Views: 1,036
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Forum: Bioinformatics
09-05-2012, 08:15 AM
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Replies: 11
Views: 3,084
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Forum: Bioinformatics
08-31-2012, 05:23 AM
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Replies: 3
Views: 4,491
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Forum: Bioinformatics
08-09-2012, 08:02 AM
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Replies: 18
Views: 15,779
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Forum: Bioinformatics
08-09-2012, 04:50 AM
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Replies: 18
Views: 15,779
Hi,
It depends on the library details, but...
Hi,
It depends on the library details, but you should could try "color by first-in-pair" from the popup menu. This will color by the strand of the template, rather than the read, at least for...
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Forum: Bioinformatics
06-13-2012, 10:22 AM
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Replies: 7
Views: 9,261
Hi,
IGV is not making any judgement calls,...
Hi,
IGV is not making any judgement calls, is is using the mapping quality. It is a convention with at least some aligners (BWA), if not all aligners, that mapping quality == 0 means the read is...
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Forum: Bioinformatics
05-17-2012, 08:05 PM
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Replies: 1
Views: 1,883
Hi Philip,
Sorry for the difficulties. We...
Hi Philip,
Sorry for the difficulties. We have had other reports of this, but sporadic. What I need is someone to work with me long enough to isolate the cause, we use it heavily here at the...
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Forum: Bioinformatics
03-13-2012, 03:13 AM
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Replies: 2
Views: 1,743
Hi,
That will work, you can also use bed...
Hi,
That will work, you can also use bed format but you have to use the extended form. See the UCSC site for details. BED files have the advantage of being much smaller, in general, and can...
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Forum: Bioinformatics
03-11-2012, 06:38 AM
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Replies: 1
Views: 1,176
Hi tia,
If your chromosome names are of the...
Hi tia,
If your chromosome names are of the form "chr1, chr2, chr3, ..." etc, you can download the following file from UCSC and just load it using "File > Load..." after selecting you custom...
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Forum: Bioinformatics
02-21-2012, 12:15 AM
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Replies: 2
Views: 2,471
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Forum: Bioinformatics
02-11-2012, 08:34 AM
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Replies: 2
Views: 4,208
Hi,
First IGV has a help forum where you are...
Hi,
First IGV has a help forum where you are more likely to get a timely response, the URL is https://groups.google.com/forum/?hl=en_US#!forum/igv-help
A couple of points (1) you don't need...
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Forum: General
02-02-2012, 07:27 AM
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Replies: 4
Views: 4,509
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Forum: General
02-02-2012, 06:55 AM
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Replies: 4
Views: 4,509
Hi Keo,
I've looked at your problem and logs...
Hi Keo,
I've looked at your problem and logs a little more, and for the sake of others who might search this forum let me clarify. I think your problem stemmed from trying to move the .genome...
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