Hi, I plan to convert SAM file into BED file using bedops sam2bed tool and perform "chr start and end coordinates" data points manipulation to break di-nucleosome and tri-nucleosome data points into mono-nucleosome data points, then convert the modified bed file back to SAM file.
My objective of bed file manipulation will have to include all other associated SAM fields as well which are used by deeptools bamCoverage for bigwig generation. All the relevant SAM fields have to be modified accordingly.
So, my question is: Which SAM or BAM file fields are used by deeptools bamCoverage for bigwig generation?
Any insight will be appreciated.
I am not sure I understand the question. deeptools will use any bam file you give it.
Sorry for the question not being clear.
Any BAM file has multiple fields (equivalent to fields in SAM file) like mentioned below:
1 QNAME; 2 FLAG; 3 RNAME; 4 POS; 5 MAPQ; 6 CIGAR; 7 RNEXT; 8 PNEXT; 9 TLEN; 10 SEQ; 11 QUAL
I want to know, which values or fields of a BAM file are used by deeptools bamCoverage or bamCompare to generate bigwig?
I will appreciate any insight on this.