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Old 02-22-2010, 05:50 AM   #1
szilva
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Default Visualizing SHRiMP mapping

Hi,

Is there a better way to look at the mapping generated by SHRiMP than its pretty-print output? I know there is a SAM converter included in the SHRiMP distribution but Tablet was not really happy with my converted files.

Cheers:
Szilva
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Old 02-22-2010, 07:59 AM   #2
drio
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Quote:
Originally Posted by szilva View Post
Hi,

Is there a better way to look at the mapping generated by SHRiMP than its pretty-print output? I know there is a SAM converter included in the SHRiMP distribution but Tablet was not really happy with my converted files.

Cheers:
Szilva
Convert to SAM and use the igv viewer from broad (http://www.broadinstitute.org/igv/).
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Old 02-22-2010, 11:32 PM   #3
szilva
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Cheers, the problem itself is the imperfect SHRiMP -> SAM conversion. Sure I can write a more reliable converter if needed with "some" effort but though others using SHRiMP had the same problem.
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Old 02-24-2010, 12:38 AM   #4
imilne
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Quote:
Originally Posted by szilva View Post
Hi,

Is there a better way to look at the mapping generated by SHRiMP than its pretty-print output? I know there is a SAM converter included in the SHRiMP distribution but Tablet was not really happy with my converted files.

Cheers:
Szilva
Any chance you could send us some example files? Tablet already has a few special cases in its various file parsers for dealing with files that don't really match the specifications (but people have nagged us to be able to view), so adding another one probably won't make much difference.

Iain
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Old 02-24-2010, 05:03 AM   #5
szilva
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Thank you indeed, unfortunately as I checked the generated SAM file, it is completely garbled. Maybe due to a sw bug or due to my inexperience. I will try to squeeze out a real SAM file from SHRiMP and if I still fail to make it work will send you a sample file.

Cheers:
Szilva
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Old 07-02-2010, 04:07 PM   #6
misko
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Hi Szilva,
Not sure if you are still interested, but SHRiMP now supports SAM output natively. There is also a nice genome browser available called Savant, that works with BAM output and works with SHRiMP.

http://compbio.cs.toronto.edu/shrimp/
http://compbio.cs.toronto.edu/savant/

Misko
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Old 07-02-2010, 10:54 PM   #7
szilva
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Cheers, indeed I am using the new (v2.x) SHRiMP for quite a while and am happy with its SAM output.
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