The phrase "amount of reads" is not correct in standard written English; it should be "number of reads." You can use it when discussing the quantity of times something has been read, typically in contexts like articles, books, or online content.
Example: "The article gained a significant number of reads within the first week of publication."
Alternatives: "total reads" or "count of reads."
The fastq files were down-sampled to the library with the least amount of reads using Seqtk (https://github.com/lh3/seqtk).
Hence, the amount of reads originating from introns of un-spliced reads is expected to depend on these characteristics of the gene.
To test if the use of a single-cell RNA dataset could uncover subtle differences in the intron retention levels of gbM and unmethylated genes, we estimated the amount of reads mapping to introns similarly to Bewick et al. (2016; see Materials and methods) and ran ANCOVA analyses to elucidate which genomic features could best predict the amount of reads mapping to introns.
Due to the possible effect derived from a different amount of reads assigned to treated water and groundwater, we modified the calculation of pi and pig such that each level would contribute equally to those estimates and not proportionally to its number of reads.
Unlike Bewick et al. (2016), here, we find a correlation between gbM and the amount of reads mapping to the introns of a gene, which points to a role of gbM in reducing RNA mis-splicing in the form of intron retention.
However, it is also possible that the observed differences in the amount of reads mapping to the introns of gbM and unmethylated genes (Table 3) could be the result of some other processes and not because of lower intron retention levels.
Indeed, our analysis revealed that the amount of reads mapping to a gene, the total intron and gene length as well as the number of introns were significantly correlated with the number of reads mapping to the introns of a gene, which was expected since RNA samples will inevitably contain un-spliced RNA (La Manno et al. 2018).
Among the more than 100 million reads from high-throughput sequencing of the 6 libraries, there was also a large amount of reads that mapped to un-annotated genomic regions.
Both Bowtie and SOAP, due to their ungapped alignment processes, were able to map only a negligible amount of reads with an insertion or deletion.
We found a significant amount of reads from the human frontal cortex originate from repeat elements.
The total amount of reads were 512,236 paired reads and 112, 079 single reads.
