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Many of these steps led to minor increases in mean insert size, but ultimately were not sufficient to provide mean insert lengths ≥100 kb.
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You mean Foley didn't ask about penis length?
In our implementation, we choose this length, denoted Ntot, to be the mean insert length plus the standard deviation of the short-insert library.
The insert statistics were estimated by aligning the remaining reads uniquely to the transcriptome and calculating the mean insert length and SD.
Important quality parameters are the number of independent clones before and after amplification, the number of clones that contain an insert and the mean insert length.
Small library fragments were removed using the BluePippin (Sage Science, Beverly, MA, USA), resulting in an estimated mean insert length of 8.4 kbp.
With such high clonal coverage we have significant power to detect evidence of discordant mate-pair reads, where the length of the insert deviates substantially from the mean insert length and/or map to different chromosomes or chromosomal regions.
In the detection of such short indels, the deviations from mean insert length are measured, and thus, the sequencing coverage required to arrive at statistical significance is inversely proportional to the indel length.
However, it was also possible to establish the position of certain clones for which only one end mapped uniquely where the other end of the clone mapped to the genome within 3 standard deviations of the mean insert length of clones from the library and on the opposite sequence strand.
Average insert lengths were determined by screening at least 300 inserts per library.
Although the mean of the insert length is 1000, the corresponding gap length in the read matrix is very small because only heterozygous SNPs are considered for assembly.
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