Many encode bam files have labels like mm10-minimal inplace of mm10 sometimes in the metadata file. I was wondering what this is. Is it mm10 with sex and non standard chromosomes removed? Also for one tissue I have multiple bam files for some output type is just alignments while others are labelled as unfiltered alignments.In the audit warning some are labelled as having low read depth or insufficient read depth. Actually I am trying to combine bam files to get a consolidated bam for a particular tissue and histone type. I am thinking that I would not use the files with insufficient read depth and/or which have mm10-minimal as their assembly and/or have unfiltered alignments. I just wanted to confirm from how other people have done it using encode data. Kindly let me know what is the most ideal way of doing this.
thanks
