column meaning of hits_accepted.sam produced from TopHat

[jiwu2573]

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

[nilshomer]

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.

[jiwu2573]

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!

[nilshomer]

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.

[jiwu2573]

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?

[nilshomer]

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.