I downloaded from the European Nucleotide Archive raw data (fastq) for human chromosome 21. It was indicated that the library is WCS and that the data is only for chr21. I mapped the data with Bowtie2 in Galaxy and I got the bam file containing all chromosomes, instead only chr 21.
So, my question is why I have all the chromosomes in my bam file?
I tried to filter that bam for only chr21, but the alignment is very bad so I suppose that this approach is not very good.
Thank you in advance.