What does the sixth column of the unstranded bed file show +-?

Question

[5Tony]

Hi all,

I recently encountered a difficulty, there is a set of unstrand data through STAR or hisat2 to get bam fileand then through bedtools bamTobed into bed file, but I found in the bed file in the sixth column (strand column) appeared '+-', unstranded bed file of the sixth column should not be '.' Shouldn't it be .

This is the expected situation:

This is the observed situation:

Thanks in advance for the help!

Answer 1

[cpad0112]

strand - Defines the strand - either ‘+’ or ‘-‘. This column is optional. Please use google.

[5Tony]

Thank you very grateful for your reply. I also found this explanation in this site, but found 'no strand=.' on another site So should we follow that?Will the strand column of the bed file only show '+-' regardless of chain specificity?

[5Tony]

Thank you very grateful for your reply. I'm sorry I got a concept wrong, I understand it now.

Answer 2

[Istvan Albert]

The strand indicates the orientation of the alignment. Not clear what the question is though.

Why do you expect it to be unstranded? Each BED record represents an alignment of a read, not the library preparation method.

[5Tony]

Thank you very grateful for your reply. I'm sorry I got a concept wrong, I understand it now.