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?
What does the sixth column of the unstranded bed file show +-?
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!
2 answers
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.
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