Difference between revisions of "SHORE File Formats"

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Latest revision as of 13:41, 20 June 2013

Any output generated by SHORE will usually be written to various text files that contain a number of tab-delimited columns.

Typing shore fmt will display a quick reference for many of SHORE’s file formats.

This page only describes SHORE's read and alignment file formats; other files formats are described on the page of the respective subprogram that generates them.

shore convert may be used to convert SHORE files into various third-party file formats, or vice versa.

SHORE FlatRead file format

Read files can be found in the LengthFolders or ReadFolders. These files are created by shore import and are named reads_0.fl.

reads_0.fl files are usually sorted on the id field in numerical order.

The tab delimited entries are:

1 id A unique identifier for the read or read pair
2 sequence DNA sequence
3 index Paired-end sequencing information - read index optionally prefixed by a single character flag:
  • 0: single end read
  • f1..fn: filter orphan - paired read or other multi part fragment whose partner/next part was lost due to quality filtering
  • t1..tn: technical read, e. g. a barcode read
  • p1..pn: paired read, neither f nor t
4 Sanger quality values String of sanger calibrated quality values

Encoding: ASCII 33 (' ! ', quality 0) to ASCII 73 (' I ', quality 40); extended range ASCII 93 (' ] ', quality 60)

5 [Chastity values]

(Optional column)

String of illumina chastity values (defined as <math>Intensity(max)/ (Intensity(max) + Intensity(second))</math>).

Encoding: ASCII 40 (' ( ', chastity of 0.5) to ASCII 90 (' Z ', chastity of 1.0)

5/6 [Tags]

(Optional column)

3-character tags in the format ~<SPACE>TAG:value;TAG:value;...;.

Valid tags are

  • BAD: bad quality read (integer)
  • BAR: resolved barcode sequence (string)
  • CLL: left clip position (integer)
  • CLR: right clip position (integer)
  • DST: read has an alignment with the given edit distance (integer)
  • RGR: read group (string)
  • NUM: number of (non-technical) reads for the template (default 2 for non-single reads, mandatory for >2 non-technical reads) (integer)

SHORE MapList file format

SHORE alignment files are typically named map.list, map.list.1 or map.list.2. They are stored in the LengthFolders or ReadFolders.

MapList files are sorted in numerical order, either on the fields chr id and pos, or on the field read id.

The tab delimited entries are:

1 chr id Each chromosome has an internal id, simply enumerated according to their occurrence within the reference sequence file, starting from 1. Translation to the native chromosome name can be found in the *.shore.ref and *.shore.trans file in the IndexFolder, or in the ref.txt files created by shore mapflowcell.
2 pos Left-most position of the alignment relative to the forward strand of the reference sequence. The first position of a chromosome is 1.
3 alignment String representation of the read alignment. The sequence is always reported with respect to the forward strand of the reference, i.e. the sequence of reads matching to the reverse strand is reverse complemented.
  • Matches are reported as a single IUPAC character
  • Mismatches or gaps as two characters surrounded by brackets. The first character represents the reference base, the second character the sequenced base. Deleted nucleotides are represented as ’-’.
    • Examples: [CT] (mismatch), [-T] (insertion), [C-] (deletion)
    • Long deletions with respect to the reference may be reported as the character L followed by the size of the deletion, e.g. [L100]
  • Unaligned sequence ('soft clip') may be reported in angle brackets, e.g. <TTTTTT>
  • Consecutive stretches of the same operation (mismatch, insertion, deletion) may be abbreviated, e.g. [CTT,---] instead of [C-][T-][T-]
  • F can be used to indicate a mapped part of a fragment with known size, but unknown sequence, e.g. [F100]
4 read id A unique identifier for the read or read pair
5 strand D for forward and P for reverse hits (direct and palindromic, respectively).
6 mismatches The number of mismatches+gaps in the alignment.
7 hits The total number of genomic positions the read is aligned to.
8 read length Length of the read ('soft clipped' nucleotides excluded).
9 offset Alignment start offset into the read (local alignments, first base of the read is 1)
  • 0: no offset, the read/query is fully aligned (soft clip is still possible)
  • ≥1: The read/query is only locally aligned and the alignment starts at the specified position. Unaligned ends are not represented in the alignment string.
10 pe flag Paired-end information - read index optionally prefixed by a single character flag:
  • 0: single read
  • f1..fn: paired read or other multi part fragment whose partner/next part was lost due to quality filtering
  • t1..tn: technical read, e. g. a barcode read
  • p1..pn: paired read, not yet paired end corrected (not 'f' or 't', but may be any of the below)
  • c1..cn: concordant mapping: distance of the partner read is in the range of the insert size distribution
  • d1..dn: discordant mapping: distance of the partner read is not in the range of the insert size distribution
  • b1..bn: suboptimal mapping: distance of the partner read is in the range of the insert size distribution, but another mapping of the read can form a more likely pairing with the same partner
  • a1..an: accessory mapping: discordant, and other mappings of the same read are concordant
  • o1..on: mapping orphan: partner is unmapped

Paired-end information was encoded differently prior to SHORE v0.8, see SHORE_v0.7_file_formats.

11 Sanger quality values String of sanger calibrated quality values, whose start corresponds to the 5' end of the read.

Encoding: ASCII 33 (' ! ', quality 0) to ASCII 73 (' I ', quality 40); extended range ASCII 93 (' ] ', quality 60)

12 [Chastity values]

(Optional column)

String of illumina chastity values defined as the highest intensity divided by the sum of the highest and the second highest intensity of a single base. The start of the string corresponds to the 5' end of the read.

Encoding: ASCII 40 (' ( ', chastity of 0.5) to ASCII 90 (' Z ', chastity of 1.0)

12/13 [Tags]

(Optional column)

3-character tags in the format ~<SPACE>TAG:value;TAG:value;...;.

Valid tags are

  • MPQ: mapping quality (integer)
  • NXP: mapping position of the next read of the template ([0-9]+:[0-9]+[DP]), valid if read is concordant or partner has a single mapping pos
  • RGR: read group (string)
  • NUM: number of (non-technical) reads for the template (default 2 for non-single reads, mandatory for >2 non-technical reads) (integer)
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