a viewer for RNAseq data

ragowthaman · 01-26-2010, 01:38 PM

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

jnfass · 01-26-2010, 02:23 PM

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 ...

jnfass · 01-26-2010, 02:25 PM

... 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.

mgogol · 01-26-2010, 02:31 PM

IGV is good. UCSC genome browser will also work directly with BAM files, but it might not be what you're after.

jnfass · 01-26-2010, 02:42 PM

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 ...

ragowthaman · 01-26-2010, 02:48 PM

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.

jnfass · 01-27-2010, 07:46 AM

... 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.

klaas.vandepoele · 01-22-2011, 07:33 AM

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

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01-26-2010, 01:38 PM	#1
ragowthaman Member Location: Seattle, USA Join Date: Nov 2009 Posts: 12	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

01-22-2011, 07:33 AM	#8
klaas.vandepoele Junior Member Location: Ghent Join Date: Jan 2011 Posts: 6	Reference GenomeView fyi, GenomeView is developed by Thomas Abeel (Ghent University, BE / Broad). For more info, check http://genomeview.org/

01-26-2010, 02:23 PM	#2
jnfass Member Location: Davis, CA Join Date: Aug 2008 Posts: 88	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 ...

01-26-2010, 02:25 PM	#3
jnfass Member Location: Davis, CA Join Date: Aug 2008 Posts: 88	... 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.

01-26-2010, 02:31 PM	#4
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	IGV is good. UCSC genome browser will also work directly with BAM files, but it might not be what you're after.

01-26-2010, 02:42 PM	#5
jnfass Member Location: Davis, CA Join Date: Aug 2008 Posts: 88	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 ...

01-26-2010, 02:48 PM	#6
ragowthaman Member Location: Seattle, USA Join Date: Nov 2009 Posts: 12	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.

01-27-2010, 07:46 AM	#7
jnfass Member Location: Davis, CA Join Date: Aug 2008 Posts: 88	... 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.