Hi, I want to subset alignments in chromosome 7 from a BAM file and write a new BAM of only chr7 alignments.

I made this:

seq3<-"HF6_1_1fragmm9.bam"
seq3reads<-readGAlignments(seq3)
seq3chr7 <- seq3reads[seqnames(seq3reads) == 'chr7']

But I dont know how can I export seq3chr7 as a BAM file, can it be done?

Thank you very much!

You could use the rtracklayer export() function. But I think you really want Rsamtools::filterBam() in this case.