If I map a bed (annotation) file onto a Strand non-specific bam file (RNA-Seq), how is it going to know the strand? I changed the strand column of bed file as in two rows with same info and different strand. But, I got the same read count for 2 rows! which means it is not looking into the strand column to check the strand. Can anyone explain how does it work then.
typically the BAM files does not contain information about the strand specificity of the original sequencing data,
when you run an analysis tool where that matters you can instruct to treat the BAM file as containing strand specific reads,
but just to make sure we are talking about the same thing, each alignment in a BAM file will contain strand information - that characterizes that specific alignment, now that strand information is different concept than what is typically "strand specific" RNA-Seq
stranded RNA-Seq means that the sequenced transcripts will be represented by a sense or antisense strand of the DNA rather than both strands
It is you, the end user, that chooses how to process a BAM file as strand-specific or not.
A tool that can handle stand-specific RNA-Seq data will produce a different output if we instruct it to treat a BAM file as strand-specific or as non-strand-specific.
So it is a choice on how a BAM file is processed, and it is not a setting inside the BAM file
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What exactly are you trying to do?
I want to know how strand non-specific bam file is mapped.
You should read about the flags used in bam files. I think you're thinking about it backwards though, you're mapping the reads from your bam file onto a bed file and not vice versa.
Oh yes. I want to know how bam file is mapped on annotation file in this case when strand is not specified.