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Old 02-04-2010, 04:53 AM   #1
gavin.oliver
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Default Problems displaying SAM file in IGV

Hi,

I am starting to play around with some NGS data and am trying to display a SAM file (e coli reads aligned to the genome) in Intergrative Genome Viewer. When I load the file no reads appear. Has anyone else experienced anyhting like this? I have imported the correct genome and checked that genome name agrees between files etc.

Any help would be appreciated!

Gavin
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Old 02-04-2010, 05:17 AM   #2
gavin.oliver
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Problem resolved!

I don't even want to admit what was happening
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Old 02-04-2010, 11:01 AM   #3
genbio64
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Dear Gavin,
I have also experienced this problem. Could you tell me how you fixed it? No doubt it is something simple that I have overlooked.
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Old 02-05-2010, 12:27 AM   #4
gavin.oliver
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I thought I had fixed it but it turns out I was wrong.

I have absolutely no idea what the issue is at all
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Old 02-05-2010, 06:04 AM   #5
krobison
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The IGV developer is a really nice guy (despite an insertional mutation in his surname :-) and is a member here; if you send him a good test case & description you are likely to get a response.
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Old 02-05-2010, 06:12 AM   #6
gavin.oliver
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Lol.

I can provide my SAM and genome file if you can give me an e-mail address?

I just can't get the alignments to display.
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Old 02-05-2010, 09:43 AM   #7
Michael.James.Clark
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Did you try zooming in? I've found it won't display if you've got high coverage and you're zoomed out far due to memory constraints.
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Old 02-05-2010, 12:06 PM   #8
krobison
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igv-help (at) broadinstitute.org is the address to get assistance
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Old 02-05-2010, 07:35 PM   #9
drio
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Quote:
Originally Posted by gavin.oliver View Post
I thought I had fixed it but it turns out I was wrong.

I have absolutely no idea what the issue is at all
Reduce your input file ((s|b)am I assume) to a one alignment. Load it and
check if it shows up. If the alignment does no show up try to change the
chrm string format. The chrm string has to match to whatever contig header
string is used in the reference you use. That was my main problem when
I started using IGV.

Ultimately the IGV mailing list is your friend.
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Old 02-08-2010, 02:45 AM   #10
gavin.oliver
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I have sent the SAM and genome files to the igv-help address. All the fixes mentioned on this thread I have already attempted (or tried to).
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Old 02-08-2010, 04:19 AM   #11
drio
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Let us know what the problem was when you find out.
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Old 10-06-2010, 01:12 PM   #12
wls.li
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Hi Gavin,

Did you end up getting a response from the guys at IGV or end up solving the problem? I seem to be experiencing the same issues. Thanks
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Old 10-07-2010, 01:18 AM   #13
gavin.oliver
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Unfortunately not!
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Old 10-07-2010, 03:52 AM   #14
jeny
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Hi Gavin,
did you try to view the alignment using an other third part tool ?
If I suggest you that, it is because I had the same problem with my SAM files, and this problem reproduced with other tools.
In my case, SAM files were converted from illumina export files using script export2sam.pl script. illumina pipeline reports file name of the sequence matched and not the fasta header of the sequence matched, whereas viewers use the header.
So, as you could anderstand if the name of the reference sequence and the name of sequence matched are not the same, softwares (IGV or others) consider that there are not reads mapped to the reference.
I don't know if you are in same case, but you could verify if field RNAME in SAM file seems ok.

Jennifer
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Old 10-07-2010, 03:56 AM   #15
gavin.oliver
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Hi Jennifer,

To be honest I haven't pursued the problem any further. Shifting priorities in my job means that I haven't been spending any time on NGS of late. It is something I may have to revisit in the future but for the time-being my hands are tied!

Sorry I can't be more help.

Gavin
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