SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Alignment to selected region of the reference genome houkto General 1 02-20-2012 05:51 AM
Targeted Genome Assembly for region poorly represented in reference genome? gumbos Bioinformatics 1 01-09-2012 04:01 PM
Galaxy cannot recognize the uploaded fastq juhang_62 Bioinformatics 3 11-11-2011 12:34 AM
IGV: display six-frame (amino-acid) translation of reference genome? d f Bioinformatics 2 03-07-2011 02:57 PM
New reference for IGV? tsucheta Bioinformatics 1 01-02-2010 06:52 AM

Reply
 
Thread Tools
Old 01-31-2012, 07:13 PM   #1
dkrtndhkd
Member
 
Location: Seoul

Join Date: Jan 2012
Posts: 42
Post How IGV recognize the reference region?

I aligned my target NGS data to chr7, not whole genome seqeunce,

when I view the result bam file by IGV,

how IGV can recognize the bam file is aligned to chr7?

the reference info is also included in the bam file?

As you might see before, the gene names which are in chr7 are also seen.

there's no gene name info in the bam file.

Curiooooooooooous!!!
dkrtndhkd is offline   Reply With Quote
Old 01-31-2012, 10:53 PM   #2
arvid
Senior Member
 
Location: Berlin

Join Date: Jul 2011
Posts: 156
Default

IGV comes with the annotation (e.g. gene locations) of some typically used genomes. When you aligned to a chr7 reference, "chr7" was stored in the BAM file. When you loaded it into IGV, IGV detected that "chr7" information and loaded the annotation for that chromosome onto the gene track...
arvid is offline   Reply With Quote
Old 02-01-2012, 07:58 AM   #3
dkrtndhkd
Member
 
Location: Seoul

Join Date: Jan 2012
Posts: 42
Default

Thankyou
dkrtndhkd 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 07:07 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO