Sentence examples for minimum read coverage from inspiring English sources

Transcripts were filtered out that had FPKM <1 for all 58 libraries using filter_fasta_by_rsem_values.pl from the Trinity package and were deemed lacking in minimum read coverage evidence to be supported.

The parameters for SNP detection in the CLC Genomics Workbench were: at least 90% probability to detect a variant, a minimum read coverage of 15 to detect a SNP, a minimum SNP count of 3, a neighborhood radius = 5, a minimum central quality = 20, a minimum neighborhood quality = 15.

Using a minimum read coverage of 10 had no effect on HIV ShoRAH results.

Similarly, reducing the minimum read coverage from 8X to 5X recovered an additional 25% of the variants.

The assembler parameters were set for a minimum read coverage of 5 and kmer size of 23 to construct reliable contigs.

The stringent minimum read coverage for each SNP was applied as a means of differentiating a sequencing error from a legitimate SNP.

To attempt to improve the quality of the SNPs selected for further analysis, selection criteria (minimum 4 read coverage, minor allele frequency (MAF) > 25%) were applied to this initial SNP set to ensure that the minor allele for all SNPs called was represented by at least 2 independent sequences.

SNPs were filtered using vcfutils.pl varFilter with minimum mapping quality (-Q) of 20 and minimum and maximum read coverage of 20 and 100 respectively.

SNPs detected by PolyPhred were filtered for quality by selecting SNPs with a minimum of 4 read coverage at the SNP position and a MAF greater than 25%.

We also empirically estimated the minimum paired/linear 454 read coverage necessary to assemble high quality sub-genomic 3 Mbp regions.

Depth of sequence coverage increases the reliability of SNP detection [ 52] and utilization of a minimum threshold for read coverage depth of 10 resulted in mapping of 93.7 %, 81.2 % and 73.3 % of the reads for P. axillaris, P. exserta, and P. integrifolia, respectively (Table  3).> Overall, there were 814,408 SNPs between the three species.