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I am not saying that popularity equates to good, quality reading.
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Now a student, I still love i because it is such a good quality read.
Good quality reads were further pre-screened for ribosomal identity (at approximately 70% identity) using Qiime-uclust and chimeras removed through UCHIME according to de novo method (Edgar et al. 2011).
Good quality reads can be obtained by linearizing the DNA between Mu ends prior to sequencing reactions (e.g. using EcoRI or XbaI).
Assessment of read quality by FastQC revealed good quality reads (data not shown).
(g) Number of reads aligned with this genome divided by the number of good quality reads.
The good quality reads were used for de-novo genome assembly.
Unmapped good quality reads were then mapped on Bos taurus genomes with Bowtie (same parameters).
Briefly, raw Illumina reads were quality trimmed and good quality reads were back mapped on the previously obtained genomic contigs.
While in this experiment 100% of the good quality reads should have mapped with their reference genome, only 80% of the good quality reads did, possibly due to sequencing errors in the reads.
This coverage however, dropped further during downstream analyses when only good quality reads were recruited for variant calling.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com