How to visualise alignments with different read lengths?

lindseyjane · 09-11-2009, 02:46 AM

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.

cariaso · 09-11-2009, 06:26 AM

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.

nilshomer · 09-11-2009, 08:49 AM

Quote:

Originally Posted by lindseyjane

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.

para_seq · 09-11-2009, 09:59 AM

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.

simonandrews · 09-14-2009, 01:18 AM

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.

lindseyjane · 09-17-2009, 02:27 AM

Thank you, I will try out these tools

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09-11-2009, 02:46 AM	#1
lindseyjane Member Location: Oxford Join Date: Apr 2009 Posts: 28	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.

09-11-2009, 06:26 AM	#2
cariaso Member Location: Wageningen, the Netherlands Join Date: Jan 2008 Posts: 31	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.

09-11-2009, 09:59 AM	#4
para_seq Member Location: Michigan Join Date: Aug 2009 Posts: 12	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.

09-14-2009, 01:18 AM	#5
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	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.

09-17-2009, 02:27 AM	#6
lindseyjane Member Location: Oxford Join Date: Apr 2009 Posts: 28	Thank you, I will try out these tools