Flags in bam file and gene strand orientation

Question

[skylinesky]

Hello, I know that if a read has SAM flag 16 means that read has been mapped to the reverse strand in bam file. My question is:

So does it mean that this read fall into the gene which is on forward strand in gene annotation files? (since gtf files are concerned with the coding sequences of genes)

Transcription of the forward-strand gene means the gene's template sequence is read from the reverse strand

Sometimes there might be different genes on both strand of DNA and I wanna know 16(for example) correspond to which gene on gene annotation files(+ or - strand gene in gtf file?)

Thanks a lot!!

Answer 1

[Pierre Lindenbaum]

So does it mean that this read fall into the gene which is on forward strand in gene annotation files

no , the BAM format doesn't care about the annotations; The read maps on the reverse strand of the REFERENCE genome.