Generated on 2023-02-11 at 16:44.

Snaptron Reference Tables

Table 1. Query Types

Query Type	Description	Multiplicity	Format	Example
Region	chromosome based coordinates range (1-based); HUGO gene name	1	chr(1-22,X,Y,M):1-size of chromosome; gene_name	chr21:1-500; CD99
Filter	range over summary statistic column values	1 or more	column_name(>:,<:,:)number (integer or float)	coverage_avg>:10
Sample Metadata	keyword and numeric range search over sample metadata	1 or more	fieldname(>:,<:,:)keyword	description:cortex; SMRIN>:8
Sample IDs	limits results to only junctions found in specified samples IDs	1	sids=\d+[,\d+]*	sids=2,40,50,100
Sample Group*	limits to only junctions found in specified sample group	1	sids=groupname	sids=Brain (gtex)
Snaptron IDs	one or more snaptron_ids	1	ids=\d+[,\d+]*	ids=5,7,8
Sample IDs	one or more sample_ids	1	ids=\d+[,\d+]*	ids=20,40,100

* The sids=groupname parameter is based on predefined groups of sample IDs. These group definitions are found in the data directory of the compilation being queried, typically in a file samples.groups.tsv, e.g. for GTEx: http://snaptron.cs.jhu.edu/data/gtex/samples.groups.tsv

The Region query type is required to be present if the Filter, Sample Metadata, Sample Group, and/or Sample IDs types are used.

Table 2. List of Snaptron Parameters

Parameter	WSI Endpoints	Values	# Occurrences	Example	Description
regions	snaptron;genes	chr[1-22XYM]:\d+-\d+;HUGO gene	1 but can take multiple arguments separated by a comma representing an OR	chr1:1-5000;DRD4	coordinate intervals and/or HUGO gene names
sids	snaptron;genes	sids=(\d+[,\d+]*)|(groupname)	1	sids=30,100,150 ; sids=Brain	filter to only junctions from >=1 samples in this list; uses the samples’ rail_ids, can also take a predefined sample group name (e.g. GTEx tissue)
ids*	snaptron;genes;samples	ids=\d+[,\d+]*	1	ids=5,6,7	ID filter for snaptron_id (endpoint=snaptron) and rail_id (endpoint=samples); this only returns the specific records with those IDs
rfilter	snaptron;genes	fieldname[><!:]value	0 or more	rfilter=samples_count>:5&rfilter=coverage_sum:3	point range filter (inclusion)
sfilter	snaptron;genes;samples	fieldname:value OR freetext	0 or more	sfilter=description:Cortex&sfilter=library_strategy:RNA-Seq	sample metadata filter (inclusion)
contains	snaptron;genes	0,1	0-1 occurrences	contains=1	return only those junctions whose start and end coordinates are within the boundaries of the region (using either coordinates directly or passed in gene name)
exact	snaptron;genes	0,1	0-1 occurrences	exact=1	return only those junctions whose start and end coordinates are match the boundaries of the region requested
either	snaptron;genes	0,1,2	0-1 occurrences	either=2	return only those junctions whose start (either=1) or end (either=2) coordinate match or are within the boundaries of the region requested
header	snaptron;genes	0,1	0-1 occurrences	header=0	include the header as the first line (or not)
fields**	snaptron;genes	fields=fieldname[,fieldname]*	0 or more unique fieldnames within one fields clause	fields=snaptron_id,samples_count	which fields to return

* The ids parameter cannot be used with other parameters.

**can include non-return field options such as: rc (result count)

Tables 3 and 4 show the queryable fields for region and range query types respectively. Fields from tables 3 and 4 can be mixed together in the same query though only one region predicate is allowed per query as specified in Table 1 above.

Table 3. Region Query Fields (“regions” parameter)

Field	Range of Values	Example	Description
coordinate*	chr(1-22;X;Y;M):1-size of chromosome	chr1:4-100	chromosome:start-end
gene symbol*	a-zA-Z0-9	CD99	HUGO (HGNC) gene symbols

*you can either pass a coordinate string or a gene symbol in the interval query segment, but not both

Often the query filter columns (Table 4) can be used as a way to reduce the number of false positive junctions. This can be done easily with the two columns: samples_count and coverage_sum. Some suggested values from our own research are presented in Table 5.

Table 4. Query Filter Fields (“rfilter” parameter)

Field	Range of Values	Example	Description
length	1-500K	intron_length<:5000	length of exon-exon junction (intron)
annotated*	0 or 1	annotated:1	whether both left and right splice sites in one or more annotations (default is both)
left_annotated*	0 or 1	left_annotated:1	whether the left splice site is in one or more annotations
right_annotated*	0 or 1	right_annotated:1	whether the right splice site is in one or more annotations
strand	+ or -	strand:+	which strand to require (default is both)
samples_count	1-Inf	samples_count>:5	number of samples in which this junction has one or more reads covering it
coverage_sum	1-Inf	coverage_sum>:10	aggregate count of reads covering the junction across all samples the junction appears in
coverage_avg	1.0-Inf	coverage_avg>:5.0	average of read coverage across all samples the junction appears in
coverage_median	1.0-Inf	coverage_median>:6.0	median of read coverage across all samples the junction appears in

* these fields are treated as booleans for the purpose of searching but as Strings when returned since if they are not 0, they will be a list of one or more annotation source abbreviations. Also, importantly, if each splice site of a junction (left/right) is annotated separately (not connected), annotated will be 0 but BOTH the left and right annotated fields will not be 0.

The return format is a TAB-delimited series of fields where each line represents a unique intron call. Table 5 displays the complete list of fields in the return format of the Snaptron web service. The chromosome, start, and, end fields are a special case where the index is a combination of all three of them together.

Table 5. Complete list of Snaptron Fields In Return Format

Field Index	Indexed?	Field Name	Type	Description
1	No	DataSource:Type	Abbrev:Single Character	Differentiates between a return line of type Intron (I), Sample (S), or Gene (G).
2	Yes	snaptron_id	Integer	stable, unique ID for Snaptron junctions
3	Yes	chromosome	String	Reference ID for genomics coordinates
4	Yes	start	Integer	beginning (left) coordinate of intron
5	Yes	end	Integer	last (right) coordinate of intron
6	Yes	length	Integer	Length of intron coordinate span
7	Yes	strand	Single Character	Orientation of intron (Watson or Crick)
8	Yes	annotated	String	If both ends of the intron are annotated as a splice site in some annotation
9	No	left_motif	String	Splice site sequence bases at the left end of the intron
10	No	right_motif	String	Splice site sequence bases at the right end of the intron
11	Yes	left_annotated	String	If the left end splice site is annotated or not and which annotations it appears in (maybe more than once)
12	Yes	right_annotated	String	If the right end splice site is in an annotated or not, same as left_annotated
13	No	samples*	Comma separated list of tuples: integer:integer	The list of samples which had one or more reads covering the intron and their coverages. IDs are from the IntropolisDB.
14	Yes	samples_count	Integer	Total number of samples that have one or more reads covering this junction
15	Yes	coverage_sum	Integer	Sum of all samples coverage for this junction
16	Yes	coverage_avg	Float	Average coverage across all samples which had at least 1 read covering the intron in the first pass alignment
17	Yes	coverage_median	Float	Median coverage across all samples which had at least 1 read covering the intron in the first pass alignment
18	No	source_dataset_id	Integer	Snaptron ID for the compilation. GTEx=1, SRAv2=2, TCGA=4)

* this field always starts with a ,; this is due to how it is searched when samples are used to filter a junction query (R+M or R+F+M). The format of this field is a comma-delimited list of samples and their raw read coverage in that sample. It uses the rail_id of the sample: ,rail_id1:coverage1,rail_id2:coverage2,.... This rail_id matches the first column in the relevant compilation’s samples.tsv file available from the links previously listed in the Raw Data and Indices section.