Output

All output files will be placed in a directory named results that will be created the first time you run bam2bakR. The output of greatest interest, the gzipped cB.csv file, will be in results/cB/. Columns that can be kept in the final cB (see the keepcols option in the config to choose among these options) are:

  • qname (read ID)
  • nA (number of As in read)
  • nC (number of Cs)
  • nT (number of Ts)
  • nG (number of Gs)
  • rname (chromosome name)
  • GF (ENSEMBL ID of gene to which read maps)
  • EF (ENSEMBL ID of gene to which read maps if read overlaps any exonic region)
  • XF (ENSEMBL ID of gene to which read maps if read only overlaps with exonic regions)
  • FR (Strandedness of read; F = forward, R = reverse. Only will have F if single-end sequencing)
  • sj (TRUE if read overlaps a splice junction)
  • ai (TRUE if read overlaps any intronic region)
  • io (TRUE if read exclusively overlaps an intronic region)
  • ei (TRUE if read maps to intronic and exonic regions)
  • TA (number of T-to-A mutations)
  • CA (number of C-to-A mutations)
  • GA (number of G-to-A mutations)
  • AT (number of A-to-T mutations)
  • CT (number of C-to-T mutations)
  • GT (number of G-to-T mutations)
  • NT (number of N-to-T mutations, where N is any nucleotide)
  • AC (number of A-to-C mutations)
  • TC (number of T-to-C mutations)
  • GC (number of G-to-C mutations)
  • NC (number of N-to-C mutations, where N is any nucleotide)
  • AG (number of A-to-G mutations)
  • TG (number of T-to-G mutations)
  • CG (number of C-to-G mutations)
  • NG (number of N-to-G mutations, where N is any nucleotide)
  • AN (number of A-to-N mutations, where N is any nucleotide)
  • TN (number of T-to-N mutations, where N is any nucleotide)
  • CN (number of C-to-N mutations, where N is any nucleotide)
  • GN (number of G-to-N mutations, where N is any nucleotide)

The tdf files to make color-coded tracks are in: results/tracks/.

Other output includes:

  • Sorted and filtered bam files in results/sf_reads/
  • HTseq output text and bam files in results/htseq/
  • SNP calls in results/snps/
  • .csv files with counts of all mutation types in results/counts/
  • Scale factors calculated with edgeR in results/normalization/