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Read_group_info.md

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Read group information

a) Sample and library tags

  • SM = biological sample name.
  • LB = name of DNA preparation library tube = {SM}.{library-specific identifier}
    (Important To identify PCR duplicates in MarkDuplicates step. Ignore in PCR free libraries)

Can be autmatically detected from current sample naming scheme:
<Sample.ID><Index.Sequence><Lane.ID><Set.number>.fastq

  • SM = <Sample.ID>
  • LB = <Sample.ID>_<Index.Sequence>

b) ID and PU (to enable merging replictes)

  • ID = Read group identifier = {FLOWCELL_BARCODE}.{LANE}
  • PU = Platform Unit = {FLOWCELL_BARCODE}.{LANE}.{library-specific identifier}. This is the most specific definition for a group of reads.

Also can be identified from the name of a sequence read in the Fastq file:
@(instrument id):(run number):(flowcell ID):(lane):(tile):(x_pos):(y_pos) (read):(is filtered):(control number):(index sequence)
FLOWCELL_BARCODE = @(instrument id):(run number):(flowcell ID)

c) Others e.g.

  • PL = Platform (Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO)

Notes:

  • One sample (SM) can have multiple libraries (e.g SE, PE50, and PE100) (LB), can run on multiple lanes and/or multiple flow cells (RGID), and can run on multiple platforms (PL).
  • One library can run on multiple lanes or multiple flow cells (PU).
  • If we have multiple samples for the same individual e.g. before and after treatment, each sample should have a different SM but unless you expect change of sequence, we can consider them multiple libraries of the same sample)
  • Multiple samples can share the same Read group ID (When manuals sya “must be unique”. They mean unique in a BAM file. So it is ok that multiple samples can share the same Read group ID)
  • if you have one library for each sample running on one lane of a sequencing machine then you can make SM=LB=RGID=PU