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Old 09-11-2009, 02:46 AM   #1
lindseyjane
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Default How to visualise alignments with different read lengths?

Hi,

Does anyone know of a tool that can be used to view alignments of short reads to a reference when the short reads are of different lengths? We have 36bp and 51bp Illumina paired end read datasets and using the LookSeq tool it has not been possible to view the reads of different length at the same time. Anone any suggestions for an alternative visualisation tool? Thanks.
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Old 09-11-2009, 06:26 AM   #2
cariaso
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http://globin.cse.psu.edu/html/docs/sim4.html

and good old clustalw
http://www.ebi.ac.uk/Tools/clustalw2/index.html

are where I'd start.
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Old 09-11-2009, 08:49 AM   #3
nilshomer
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Quote:
Originally Posted by lindseyjane View Post
Hi,

Does anyone know of a tool that can be used to view alignments of short reads to a reference when the short reads are of different lengths? We have 36bp and 51bp Illumina paired end read datasets and using the LookSeq tool it has not been possible to view the reads of different length at the same time. Anone any suggestions for an alternative visualisation tool? Thanks.
There is a basic text viewer in SAMtools as well.
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Old 09-11-2009, 09:59 AM   #4
para_seq
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You might want to try Broad Institute's Integrative Genomics Viewer (IGV) (http://www.broadinstitute.org/igv/). Among other things, it enables the visualization of the mapped reads with the reference genome sequence and a feature table. No complicated installation steps to take.
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Old 09-14-2009, 01:18 AM   #5
simonandrews
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You can also do this with SeqMonk. Just select the genome you aligned against, point it at your sorted or export file from Eland and off you go.
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Old 09-17-2009, 02:27 AM   #6
lindseyjane
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Thank you, I will try out these tools
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