View TopHat output

xiaohua · 01-10-2012, 07:21 PM

I want to get alternative splicing in the organism which I was researched,I have the genome sequences(it is unpublished) and RNA-Seq data ,I have use TopHat and get some output files(.bam , .bed files),but I don't know how to see the results,If I want to get the alternative splicing,what should I do ? I have read the TopHat manual and it said that I should use IGV,IGB or UCSC Genome Browser to see the result,I have downloaded IGV,what was the file I should import to IGV,genome sequence or the genome annotation file? and which is the output file I should import?Does anyone can help me ?

capricy · 04-11-2012, 02:57 PM

I have the same question. Got the results, but don't understand what is going on...

xiaohua · 04-11-2012, 06:11 PM

I have solved the problem.

You can use the IGV to view the result,the TopHat output file .bam file is the reads mapping file,if you import this file to the IGV,you can see how the reads was mapping to the genome sequence,but before you import the .bam file to the IGV,you should use SAMtools command ‘index' to index it.The .bed file is the junction file,you can see the splice site in the IGV after you import the file to it directly.You can see how to use the IGV in its website,and you will see how to see the junction information.

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01-10-2012, 07:21 PM	#1
xiaohua Junior Member Location: China NanJing Join Date: Jan 2012 Posts: 2	View TopHat output I want to get alternative splicing in the organism which I was researched,I have the genome sequences(it is unpublished) and RNA-Seq data ,I have use TopHat and get some output files(.bam , .bed files),but I don't know how to see the results,If I want to get the alternative splicing,what should I do ? I have read the TopHat manual and it said that I should use IGV,IGB or UCSC Genome Browser to see the result,I have downloaded IGV,what was the file I should import to IGV,genome sequence or the genome annotation file? and which is the output file I should import?Does anyone can help me ?

04-11-2012, 02:57 PM	#2
capricy Senior Member Location: 63130 Join Date: Apr 2012 Posts: 125	I have the same question. Got the results, but don't understand what is going on...

04-11-2012, 06:11 PM	#3
xiaohua Junior Member Location: China NanJing Join Date: Jan 2012 Posts: 2	I have solved the problem. You can use the IGV to view the result,the TopHat output file .bam file is the reads mapping file,if you import this file to the IGV,you can see how the reads was mapping to the genome sequence,but before you import the .bam file to the IGV,you should use SAMtools command ‘index' to index it.The .bed file is the junction file,you can see the splice site in the IGV after you import the file to it directly.You can see how to use the IGV in its website,and you will see how to see the junction information.