SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to combine junctions.bed files produced by TopHat HTS Bioinformatics 8 05-03-2015 02:33 AM
what files are produced from CNVnator ? Kennels Bioinformatics 1 01-23-2012 08:14 AM
meaning of every column of accepted_hit.bam from tophat chenyao Bioinformatics 7 08-12-2011 08:26 AM
the meaning of CIGAR column in SAM file outputs by BWA holywoool Bioinformatics 2 01-04-2011 04:34 AM
Different results produced by tophat? kentnf Bioinformatics 2 10-29-2010 09:35 AM

Reply
 
Thread Tools
Old 03-07-2010, 07:36 PM   #1
jiwu2573
Member
 
Location: Australia

Join Date: Jun 2009
Posts: 34
Default column meaning of hits_accepted.sam produced from TopHat

I copied one row from the hits_accepted.sam and try to understand the meaning of each column as there is no header in this file.

Can anyone knows help to explain what each column actually means?

Thanks in advance

GAPC:1:78:1727:245#0 0 chr1 554341 3 75M * 0 0 GTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATT a_YaYYaaa[`US\ZW^a`[T]N]_^^`^Xa]\^a][[]aY\\\UZ_`a^`[]Y]^^`SURXZSZTLPSFVaM_U NM:i:0
jiwu2573 is offline   Reply With Quote
Old 03-07-2010, 09:26 PM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by jiwu2573 View Post
I copied one row from the hits_accepted.sam and try to understand the meaning of each column as there is no header in this file.

Can anyone knows help to explain what each column actually means?

Thanks in advance

GAPC:1:78:1727:245#0 0 chr1 554341 3 75M * 0 0 GTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATT a_YaYYaaa[`US\ZW^a`[T]N]_^^`^Xa]\^a][[]aY\\\UZ_`a^`[]Y]^^`SURXZSZTLPSFVaM_U NM:i:0
Take a look at the SAM specification.
nilshomer is offline   Reply With Quote
Old 03-08-2010, 12:34 PM   #3
jiwu2573
Member
 
Location: Australia

Join Date: Jun 2009
Posts: 34
Default

Yeah, I did look at the specification.

But the specification mentions too many things that actually don't exist in my file, which turns out to be confusing.

Can you point out which column in my file corresponds to which part in the specification document?
That will be great help.

Thanks!

Last edited by jiwu2573; 03-08-2010 at 12:40 PM.
jiwu2573 is offline   Reply With Quote
Old 03-08-2010, 01:06 PM   #4
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by jiwu2573 View Post
Yeah, I did look at the specification.

But the specification mentions too many things that actually don't exist in my file, which turns out to be confusing.

Can you point out which column in my file corresponds to which part in the specification document?
That will be great help.

Thanks!
Section 2.2.1. Please read it carefully.
nilshomer is offline   Reply With Quote
Old 03-08-2010, 06:44 PM   #5
jiwu2573
Member
 
Location: Australia

Join Date: Jun 2009
Posts: 34
Default

Roughly understand it now.

How about the 2nd column?

It is bitwise flag, the table shows 0*0001, 0*0002, etc, but my data is "0" or "16".

How do my data relate to the flag table?
jiwu2573 is offline   Reply With Quote
Old 03-08-2010, 07:10 PM   #6
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by jiwu2573 View Post
Roughly understand it now.

How about the 2nd column?

It is bitwise flag, the table shows 0*0001, 0*0002, etc, but my data is "0" or "16".

How do my data relate to the flag table?
You can use the "samtools view -X" option to convert the number into a parsable string. Alternatively, you have to convert the decimal number to its binary representation and go from there.
nilshomer 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 08:25 PM.


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