#Clc genomics workbench reads to low full

Note that in many open source tools users are required to specify the maximum intron size. Matches that are found further away from the seed than this value are discarded.

Maximum distance from seed is the maximum distance allowed between the first match part (the seed) and any subsequent match part (non-seed segments).

#Clc genomics workbench reads to low full

If the seed makes up the full read it may map in up to 'Maximum number of hits' positions.

If it is not exceeded, all the multiple hit positions will be considered. If, for a non-seed segment, this number is exceeded, the read is classified as unmapped. Maximum number of hits for a segment is the maximum number of hits that a segment is allowed to have in order for the read to be mapped.3: Specify the parameters for the Large Gap Read Mapping tool. In the Mapping options dialog, specify the following parameters (figure 2.3):įigure 2. 2: Selecting references for the Large Gap Read Mapping tool. In the next dialog, specify the reference (a sequence track or a sequences list) to which the reads should be mapped (figure 2.2):įigure 2. 1: Selecting references and specifying parameters for the Large Gap Read Mapping tool. Toolbox | RNA-Seq Analysis ( ) | Transcript Discovery ( ) | Large Gap Read Mappingįirst specify the RNA-Seq reads that should be analyzed (figure 2.1):įigure 2. The Large Gap Read Mapping tool is started from the Toolbox: Matched regions found in later rounds are called non-seed segments. The matched region of the read identified in the first round of the mapping is called the seed segment (or just 'seed'). For full-length transcripts more than ten rounds may be required. For short 100 bp reads the maximum will usually be maximum three rounds of mapping (corresponding to spanning two introns). The number of rounds required scales with the length of the reads. This continues until no reads have unaligned ends that are longer than 15 bp.If there is an unaligned end which is long enough for the mapper to handle (15 bp for standard mapping), this part of the read is used as input to step 1.If the match is good enough (according to the settings, see below), the read is mapped to this position.The Large Gap Read Mapping tool works by iteratively applying the standard read mapper of CLC Genomics Workbench to each read as follows: It is developed to support transcript discovery using RNA-Seq data, since it is able to map RNA-Seq reads that span introns without requiring prior transcript annotations. The Large Gap Read Mapping tool maps reads to a reference, while allowing for large gaps in the mapping.