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Attempts were made to further investigate regional patterns by computing and mapping percentages and percentage changes for each category (single and never-married) using 2003 and 2013 data.
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Graphical representation of these mapping attributes, mapping percentage and mapping speed, for both aligners and a comparison between the handling of raw data and quality data is shown in Figure 1.
We compared differences in unique read counts and mapping percentages between rheMac2 and MacaM assemblies using a paired T-test.
Using the same target region and RainDance amplicon library on different NGS technology platforms resulted in opposite numbers of produced reads and mapping percentages to the human genome (Table 1 and Additional file 3: Table S6).
The comparable RNA-seq read mapping percentages of the B6 and the non-B6 strains (Table 1), suggests that near-optimum alignment for each strain was achieved using the B6 reference genome; however great care must still be taken to reduce or avoid potential alignment artifacts stemming from aligning non-B6 RNA-seq reads to the B6 genome.
TS produced the best mapping percentages to the CDS sequences (72 and 77%), followed by OV and SMART (61 to 65%) (Table 2).
These high mapping percentages indicate that these sequences were not assembly artifacts and that they might correspond to co-purified genomic fragments or immature transcripts.
Mapping percentages are relative to Paired l32q20.
Similar mapping percentages were achieved using another mapping tool, Bowtie2 [ 28] (data not shown).
Reads that mapped to intergenic or non-coding DNA were not included when determining these mapping percentages.
To increase the mapping percentages of tag sequences, two different reference databases were employed, which included G. raimondii genome and G. arboretum genome.
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