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For example, in mouse brain tissue, 20,945 non-consecutive exon junctions (skipped junctions) were supported by RNA-seq reads, of which 86.34% (18,088/20,945) were covered only by one read (Figure S3).
Sequencing of 3264 cDNAs from the 5' end yielded 3020 sequence reads, of which ∼34% (1019) shared no significant similarity to mitochondrial or bacterial genomes, and met a 70-bp length threshold after end-trimming and vector screening.
The reads were assembled with Mira 2.9.15 [9] to create 18,103 contigs (average length of 253 bp) using 149,406 reads, of which 1,039 contigs were at least 500 bp in length, similar to that obtained by 454 pyrosequencing in other insects such as M. cinxia [8] and the six-spot burnet moth, Zygaena filipendulae [10].
Through these analyses, we obtained 34,409,110 reads, of which 76.47% had quality index ≥30.
b HQ mapped number of high quality reads of which mapping quality score ≥ 30.
This corresponded to 15.21 and 16.62 million reads of which 90.63% and 35.37% passed filter, respectively.
This corresponded to 16.53 million and 16.21 million reads of which 72.58% and 73.31% passed filter, respectively.
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Thirty-eight full text articles were read, of which 31 did not meet the inclusion and exclusion criteria and therefore seven studies were retained for data extraction (see Figure 1).
Reads removed in these processes accounted for about 35% of all reads, most of which represented reads lacking PCR primer sequences (Supplementary Table S2).
Approximate 79% of the unassembled reads can hit more than 10 other reads, 55% of which hit more than 100 other reads.
For the WT ChIP Material, there were 31,424,233 total reads, 30331510 of which passed filtering and 16,780,814 reads which mapped to uniquely.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com