SeqCode mainly analyzes the set of mapped reads of a sequencing experiment (e.g. ChIPseq/RNAseq/ATACseq) in
format. This file format contains one line per read
that is mapped, containing the location in the genome for such a read. BAM files, which are the compressed version
of SAM files, can be also provided to SeqCode. For further information, users can access the SAM format documentation at
This is an extract of a SAM file from the mapping of a ChIPseq experiment:
Implementation notes (SeqCode requirements):
- SAM/BAM files should exclusively contain aligned reads (unmapped reads with flag=4 must be removed).
- SAM/BAM file indexing and sorting is not required to perform SeqCode analyses.