This section outlines the general structure of the data from SOLiD
based sequencers.
Structure of SOLiD run names
For multiplex fragment sequencing the run names will have the form:
<instrument-name>_<date-stamp>_FRAG_BC[_2]
(For example: solid0123_20110315_FRAG_BC
).
The components are:
<instrument_name>
: name of the SOLiD instrument e.g. solid0123
<date-stamp>
: a date stamp in year-month-day format e.g. 20110315
is 15th March 2011
FRAG
: indicates a fragment library was used
BC
: indicates bar-coding was used (note that not all samples in the
run might be bar-coded, even if this appears in the name)
2
: if this is present then it indicates the data came from flow cell
2; otherwise it’s from flow cell 1.
For multiplex paired-end sequencing the run names have the form:
<instrument-name>_<date-stamp>_PE_BC
Here the PE
part of the name indicates a paired-end run.
Note
If the run name contains WFA
then it’s a work-flow analysis and not
final sequence data.
See also SOLiD 4 System Instrument Operation Quick Reference (PDF)
for more information.
Navigating SOLiD run data directories
Run definition file
Typically the top-level of a SOLiD run data directory should contain the run
definition file which has information about the samples and libraries used in
the run, including the names that were assigned when the run was set up. For
example for a bar-coded sample this might look like:
version userId runType isMultiplexing runName runDesc mask protocol
v1.3 lab_user FRAGMENT TRUE solid0127_20111013_FRAG_BC 1_spot_mask_sf SOLiD4 Multiplex
primerSet baseLength
BC 10
F3 50
sampleName sampleDesc spotAssignments primarySetting library application secondaryAnalysis multiplexingSeries barcodes
DB_SB_JL_pool 1 default primary DB01 SingleTag sacCer2 BC Kit Module 1-96 "1"
DB_SB_JL_pool 1 default primary DB02 SingleTag sacCer2 BC Kit Module 1-96 "2"
...
DB_SB_JL_pool 1 default primary SB_DIMB_2 SingleTag none BC Kit Module 1-96 "14"
DB_SB_JL_pool 1 default primary SB_DMTA SingleTag none BC Kit Module 1-96 "15"
Essentially the run definition file consists of a three sections, each
delimited by a header line. The last section (with the header line
beginning sampleName...
) has the information on each of the libraries,
and can be used to locate the primary data files.
Primary data files (csfasta/qual) for multiplex fragment sequencing
Locating the primary data files within the SOLiD data directories can be
quite tedious and confusing. For bar-coded samples the following heuristic
can be used:
From the top-level of the SOLiD run directory (e.g.
solid0123_20111013_FRAG_BC
) move into the subdirectory with the sample
name of interest (e.g. DB_SB_JL_pool
, from the run definition file in
the previous section).
Within the sample subdirectory, look for a directory called results
(which will be a link to one of the other results...
directories here).
Move into the results
directory.
Within the results
subdirectory, look for a directory called
libraries
and move into this.
Within libraries
you should see subdirectories named for each of the
libraries associated with this sample, as they appear in the run definition
file (e.g. DB01
, DB02
, …, SB_DIMB_2
, SB_DMTA
). Move into
the subdirectory for the library of interest.
Within the directory for a specific library, there should be one or more
subdirectories with names of the form primary.20111015000420127
(and
possibly also secondary.20111015000420127
). Check each of these
subdirectories looking for the one which itself contains three subdirectories
reads
, rejects
and reports
(the others will only contain
reads
and reports
). Move into this directory, and then into the
reads
subdirectory. This is the location of the primary data files
(csfasta and qual files).
Typically this results in a path of the form:
solid0123_20111013_FRAG_BC/SAMPLE_NAME/results/libraries/LIBRARY_NAME/primary.TIMESTAMP/reads/
As a further check, the primary data file names should include F3
in the name.
Primary data files (csfasta/qual) for multiplex paired-end sequencing
In the case of paired-end sequencing the final data consists of primary data
file pairs for both the F3
and F5
reads for each library.
Locating the F3
and F5
reads uses a similar heuristic to that
described above for multiplex fragment sequencing:
From the top-level of the SOLiD run directory, move into the subdirectory
for the sample name of interest (e.g. DB_SB_JL_pool
).
Look for the results
directory and move into it.
Look for the libraries
directory and move into it.
Within libraries
there are subdirectories for each of the libraries
associated with this sample (e.g. DB01
, DB02
, …, SB_DIMB_2
,
SB_DMTA
) - move into the one for the library of interest.
Here there are one or more subdirectories with names of the form
primary.20111015000420127
etc. Check each of these subdirectories
looking for those which contain three subdirectories reads
, rejects
and reports
(not just reads
and reports
). There should be two
primary...
directories which match this criterion: in the reads
directory of one there will be primary data files with F5-BC
in the
name, and in the other files with F3
.
Automatic location of primary data using analyse_solid_run.py
The heuristics described above are also encoded in the
analyse_solid_run.py
program, which will identify and report the location of the primary data
files when without any other arguments i.e.:
analyse_solid_run.py solid0123_20111101_FRAG_BC
This works for both multiplex fragment and multiplex paired-end sequencing.