FAQ       Help    BAM file sort order Question ID 106 Category Qlucore Omics Explorer   Analysis Date Created 2015-04-29 08:34:38 Date Updated 2015-04-29 08:43:30 I’m getting the error "BAM file not sorted by coordinate", although I'm sure my BAM files are already sorted on coordinate. Answer Qlucore Omics Explorer determines the sort order by the BAM file header information (the '@HD-SO:coordinate' tag). But not all sorting tools add the proper information to the header. In particular, older versions of samtools had this issue. But in more recent versions the problem with the missing/erroneous sort header has been fixed. See http://www.htslib.org/doc/samtools-1.1.html, and the entry on 'sort'. If you are sure your files are correctly sorted an alternative to resorting with a newer tool is to manually change the header to contain the correct tag. E.g if the header reads something like "@HD VN:1.4" change it to "@HD VN:1.4 SO:coordinate". Related articles Biosulfite sequencing ChIP-seq and ATAC-seq How are counts counted when importing bam files? How does Qlucore calculate the length of the gene to do the normalization? How to import data (RNA-seq, Illumina, Affymetrix, 10x, Agilent, Wizard, tab separated, csv, txt, bam) Low expression levels RNA-seq data filtering RNA-seq normalization for BAM files Working with RNA-seq data (bam) Was this information helpful?   Back to Search Results