What does the sixth column of the unstranded bed file show +-?
2
0
Entering edit mode
7 weeks ago
5Tony • 0

Hi all,

I recently encountered a difficulty, there is a set of unstrand data through STAR or hisat2 to get bam file, and 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:

enter image description here

This is the observed situation:

enter image description here

Thanks in advance for the help!

bam unstranded RNA-seq bedtools star • 406 views
ADD COMMENT
1
Entering edit mode
7 weeks ago

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

ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
7 weeks ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2221 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6