SAM format is read-centered and, in CRAC’s philosophy, we do not see a read as a whole. Rather, it considers portions of the read. Hence, we propose homemade formats for CRAC to classify all breaks for each read. In other words, a same read can be classified[1] several times in different files.

Description of each field

In each homemade format, there are some header lines. In each header line, there are some field and it is not easy to understand these fields without any explanation. This is a description of the fields.

First of all, in every field, when we talk about position pos or location loc, the position or the location always start at 0.

  • read_id is the read number in input file. In case of paired reads, numbers for readid are interlaced, ie. 0,2,4,…,N-2 for reads of the first paired file and 1,3,5,…,N-1 for the second paired file.
  • single_loc_on_genome is the coordinate chr strand,relativepos of a representative k-mer on the reference index. In fact, this coordinates identify the location of the read on the reference index used for the mapping process.
  • occurrence_loc_on_genome is the same as above except that no representative k-mer with a single loc has been found, so one of the multiple locations was given.
  • pos_single_loc_on_read is the position of the k-mer used for the single_loc_on_genome in the read.
  • read corresponds to the nucleotide sequence of the read.
  • p_support represents a profile of all k-mers support along the read.
  • p_loc represents a profile of all k-mers location (number of locations on the reference for each k-mer) along the read.
  • pos_start_repeat_on_read is the position that corresponds to the beginning of a repeated factor in the read. A repeated factor is a factor which is located inside a repeated region on the reference index.
  • pos_end_repeat_on_read is the position that corresponds to the end of a repeated factor in the read.
  • tag_snv, tag_indel, tag_splice or tag_chimera is a tag to indicate if the biological event is ambiguous or not. Tag with a value to “single” means that the event is unique and a tag with a value to “duplicate” means that the event is ambiguous.
  • score is a score given by CRAC to give a relevance for a sequence error or a biological event. The threshold is 0, a negative score means that a biological event is found while a positive score means that a sequence error is found.
  • snv is a chain composed by two nucleotides and the symbol “->”. The first nucleotide corresponds to the reference index and the second corresponds to the read.
  • loc_snv_on_genome is the location of the k-mer on the genome immediately before the snv.
  • pos_snv_on_read is the position of the snv on the read.
  • splice_length corresponds to the length of the splice, ie. the distance between the end of the first exon and the start of the second exon.
  • loc_end_first_exon_on_genome is the location of the last k-mer located just before the junction, ie. the last k-mer of the first exon.
  • loc_start_second_exon_on_genome is the location of the first k-mer located just after the junction, ie. the first k-mer of the second exon.
  • pos_junction_on_read is the position of the junction in the read.
  • bioUndetermined_cause_features or undetermined_cause_features is a message to indicate why the break could not be classified somewhere above.
  • chimera_class is a flag to explain why we have classified a biological event as a chimera. This flag is described by the following table.
  • chimera_score is a score to explain the relevance of the chimera. It ranges between 0 and 1. Minimal score for stringent-chimera is 0.6.

    Flag Description
    1 The exons are located on different chromosomes.
    2 The exons are colinear but (likely) belong to different genes; this must be checked with annotation.
    3 The exons are on the same chromosome and same strand, but not in the order in which they are found on DNA, and they do not overlap each other.
    4 The exons are on the same chromosome but on different strands.

[1] We cannot properly talk about classification, since a read may contain at the same time a SNP, a splice junction and a sequencing error. Therefore it can be “classified” in three different places. However we use the term classification as it is more convenient.