SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
bcftools view generates an empty output manore Bioinformatics 14 07-08-2016 03:19 AM
Can I view output the entire genome data? ardmore Bioinformatics 6 11-09-2011 02:21 PM
AMOS: problem getting hawkeye to view bambus output Kennels Bioinformatics 3 08-24-2011 08:49 PM
samtools view error: CIGAR and sequence length are inconsistent (tophat/bowtie) glacierbird Bioinformatics 2 06-29-2010 02:58 AM
tophat - cannot view sam output in samtools tview lmilne Bioinformatics 2 12-01-2009 01:13 PM

Reply
 
Thread Tools
Old 01-10-2012, 07:21 PM   #1
xiaohua
Junior Member
 
Location: China NanJing

Join Date: Jan 2012
Posts: 2
Default 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I want to get alternative splicing in the organism which I was researched,I have the genome sequences(it is unpublished) and RNA-Seq data ,I have use TopHat and get some output files(.bam , .bed files),but I don't know how to see the results,If I want to get the alternative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 ?
xiaohua is offline   Reply With Quote
Old 04-11-2012, 02:57 PM   #2
capricy
Senior Member
 
Location: 63130

Join Date: Apr 2012
Posts: 125
Default

I have the same question. Got the results, but don't understand what is going on...
capricy is offline   Reply With Quote
Old 04-11-2012, 06:11 PM   #3
xiaohua
Junior Member
 
Location: China NanJing

Join Date: Jan 2012
Posts: 2
Smile

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.
xiaohua is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:45 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO