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Old 01-26-2010, 01:38 PM   #1
ragowthaman
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Default a viewer for RNAseq data

Hi All,
We have done a RNAseq and aligned the reads against the genome (there is no introns in here) using bowtie. I also have BAM/SAM output files. I am looking for a viewer to view the alignment.

I tried MapView. Works good. But, there is no way to display the genome annotation information

others like signalmap, artemis display only the coverage but not the reads themselves. ANy suggestion. I tried lookseq. I have problem setting that up.

Gowtham
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Old 01-26-2010, 02:23 PM   #2
jnfass
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IGV (integrated genomics viewer, from Broad) will display the read alignments, as well as variant positions (without relying on samtools for variant calling) from a bam file ...
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Old 01-26-2010, 02:25 PM   #3
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... as well as annotation from bed or other file formats (gff, I think?) ... and it displays coverage at certain zoom levels automatically, and you can run a 'count' tool within 'igvtools' that will give you a file that allows you to view (binned) coverage at all zoom levels.
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Old 01-26-2010, 02:31 PM   #4
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IGV is good. UCSC genome browser will also work directly with BAM files, but it might not be what you're after.
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Old 01-26-2010, 02:42 PM   #5
jnfass
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re: IGV versus UCSCGB ... with IGV it's a snap to set up and run with your own (non-standard) genome. Also, you can view all "chromosomes" (or scaffolds) of your genome at the same time, lined up .. something you can't do with UCSC unless you specifically create a "fake-o-some" fasta file. On the other hand, UCSCGB has table queries, and can link with Galaxy for complicated feature counting / overlap / etc. analysis ...

pro's and con's ...
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Old 01-26-2010, 02:48 PM   #6
ragowthaman
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Hi both,
Thanks for the quick replies. Does the Broad institute has two such tools? GenomeView and Integrated Genome View. It seems IGV needs some conversions.....while at it, i tried genomeview. It worked too. May be IGV is an improved version of Genomeview.

I will update how my IGV goes. Thanks again.
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Old 01-27-2010, 07:46 AM   #7
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... hadn't heard of genomeview. Must be a different group within Broad? In any case, if you try and compare both, please let us (here on the forum) know what you think.
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Old 01-22-2011, 07:33 AM   #8
klaas.vandepoele
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Default Reference GenomeView

fyi, GenomeView is developed by Thomas Abeel (Ghent University, BE / Broad).
For more info, check http://genomeview.org/
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