From: Mason Meyer <mmeyer20@uncc.edu>
To: Rajesh Biswas <biswasr0@gmail.com>
CC: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Date: Wed, Sep 20, 2017 at 10:26 AM
Subject: Re: view read sequence

Hello Rajesh,

My name is Mason Meyer, IGB Support Specialist. Thank you for contacting us with your question. After viewing the screenshots you sent, it appears to me that your files are BED files and the "View Read Sequence" feature will only work for BAM files containing read alignments.

For your case, the "View Genomic Sequence" option should allow you to view the selected peak's sequence. If that allows you to accomplish your goal, please let me know and I will mark your issue as resolved, but if not, please don't hesitate to contact me and I will continue to look into the issue. Also, if you have any additional feedback for our team, we would love to hear it!

Thanks again,

Mason Meyer
IGB Support Specialist

From: Rajesh Biswas <biswasr0@gmail.com>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Wed, Sep 20, 2017 at 10:48 AM
Subject: Re: view read sequence

Hi, Mason
thanks for your reply, yes I can do view genomic sequences to get the "genomic" sequence of the corresponding peak, but dont know if this sequence is true peak sequence, in my impression the genomic sequence come from reference seq loaded and corresponds up to the area of the peak, this sequence can be taken as consensus of the peak. Is there other way by which I can get the sequence of the peak from BED file ? please suggest

Thank you
Rajesh

From: Mason Meyer <mmeyer20@uncc.edu>
To: Rajesh Biswas <biswasr0@gmail.com>
CC: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Date: Wed, Sep 20, 2017 at 11:43 AM
Subject: Re: view read sequence

Hello again Rajesh,

That is an excellent question. As I understand it, the BED format does not contain any sequence data so IGB would not be able to retrieve any sequence data from the BED file. With that being said, my knowledge of peak data is somewhat limited, so I am going to run your question by the rest of our team to see if they can give me a solid answer on this.

While reviewing your issue, I did run across a question asked in a forum that sounds similar to what you are doing. I have sent a link to it below because it may give you an idea of how you can extract the peak sequence from your files. If this helps in any way, please let me know. In the meantime, I will check your question with my other team members.

https://groups.google.com/forum/#!topic/macs-announcement/vuvNT1IuiRA

Thanks again,

Mason Meyer
IGB Support Specialist

From: Rajesh Biswas <biswasr0@gmail.com>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Wed, Sep 20, 2017 at 4:33 PM
Subject: Re: view read sequence

Hi, Mason
thanks for your suggestion, I can extract sequences using bedtoos, thats fine, but just wanted to view with respect to corresponding peak in some visualization tool like IGB, wondering if that is possible
otherwise I have sequences corresponding to each peaks in other file and can always refer to the peak that i am visualizing
Thank you
Rajesh

From: Mason Meyer <mmeyer20@uncc.edu>
To: Rajesh Biswas <biswasr0@gmail.com>
Date: Fri, Sep 22, 2017 at 12:31 PM
Subject: Re: view read sequence

Hello again Rajesh,

Unfortunately, I don't believe you will be able to view the sequence using a BED file, since no sequence data will be contained in it. It is possible that the program that output your BED file used one of the BED file's columns to include the sequence data, but I have personally never seen this. If you would like to share your file with me, I would be happy to check it out for you and tell you if it contains any sequence data, but it most likely does not. You could also open the file in a text editor and if you see what looks like sequence data, let me know and I can assist you in viewing this info in IGB by viewing the peak's selection info (this info is also contained in the tooltip when you hover on an annotation in IGB).

If you have any other questions or feedback, please don't hesitate to contact me.

Sincerely,

Mason Meyer
IGB Support Specialist