Sentence examples for based on read length from inspiring English sources

Considerably complicating incorporation of genome-wide base-by-base mappability into analysis of NGS reads is the fact that such maps must ideally be specifically tailored based on read length, alignment algorithm and alignment parameters, since these parameters will all influence whether a read will be considered mappable.

The raw reads were aligned using the STAR algorithm (version 2.3.0e) [ 12] to the human reference genome (hg19), allowing a total of 2%% mismatches based on read length within the matched sequence.

The unigene set was then further analysed for quality based on read length, and any remnant sequences less than 100 bp in length were excluded from further analysis, leaving a total of 15,354 contigs and 66,652 singletons.

During the alignment, the "-m" setting for mismatches was set at default to allow GSNAP to auto set the number of allowed mismatches based on read length, which allowed for the best alignment across intron-exon boundaries GSNAP "soft-trims" reads during the alignment process, so that only portions of the reads above the quality threshold are aligned.

The unigene sets were then further assessed for quality based on read length, and any remnant sequences less than 100 bp were excluded from further analysis, leaving a total of 13,583 contigs and 57,099 singletons (field pea) and 6,351 contigs and 54,089 singletons (faba bean).

Alternatively, tools based on read coverage can detect duplicated insertions of any length by finding reference segments that have higher read depth than expected.

We show that under a varying read length this mixture approach provides a more stable estimation of taxonomic composition than methods based on read classification.

Secondly, the sequencing data from the cycloheximide-treated sample were used to calculate overall coverage (based on total read length) and an RPKM value.

Because we intended to use a next-generation sequencer for the validation study, we selected the CpG sites to be examined based on the read length restriction of the sequencer.

In our method, this is resolved by simply interrupting the poly-T region with a single C. A single copy of this 'broken-T' adaptor was found in 98,276 of the raw reads (16% of the total), slightly more than the expectation (~10%) based on average read length (232 bp) and assuming an average transcript size of 2,200 bp.

First, Cufflinks fragments per-kilobase of exonic length per million base pairs mapped (FPKM) expression values were validated against SailFish, an alignment-free quantification method that uses K-mers and defines expression levels based on reads per-kilobase of exonic length per million base pairs mapped (RPKM) [ 39].