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The study I most recently read was done by Calvert, a sustainable mutual fund company, and George Serafeim, a professor at the Harvard Business School.
The identification of the AGI by a read was done via the MIRA unigenes and their best BlastX hit against the Arabidopsis proteome (TAIR9) [ 65].
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Quality assessment of reads was done using read quality filtering tool, filteR [ 24].
Pre-processing of reads was done with standard protocols (see Materials and Methods).
The normalization of the absolute values of the number of reads was done based on [ 48].
The removal of poor-quality reads for mRNA-seq reads was done in the same way as sRNA analysis.
The adaptor trimming for the small RNA-seq reads was done in the same way as for the mRNA reads.
Analysis of sequencing reads was done using Tophat software [ 18] for alignment with the reference genome (btau4.0).
Demultiplexing and removal of 6 bp barcode in 51-bp reads was done with Novobarcode software (Novocraft Technologies, Selangor, Malaysia).
Quality control of the raw sequencing reads was done for each library using the program FastQC [ 45].
Subsequent analysis of sequence reads was done using miRNAkey, a tool for miRNA differential expression analysis [ 18].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com