The phrase "alignment and counting" is correct and usable in written English.
It can be used in contexts where you are discussing the arrangement or organization of items and the process of tallying or quantifying them.
Example: "The alignment and counting of the data points were crucial for the accuracy of the final report."
Alternatives: "arrangement and tallying" or "organization and enumeration".
This approach allowed students to focus on principles of read alignment and counting through a series of guided exercises in worksheet 3 and on discovering differentially expressed genes in worksheet 4. Students worked with files containing raw gene counts for two abiotic stresses and control samples for two genotypes generated by the instructor (see Data Set 1 in the Supplemental Material).
It minimised the variations, secondary to read alignment and counting, by employing the same spliced aligner (Tophat2) [ 16] and counting algorithm (HTSeq 0.5.4) [ 17] for all methods, except for Cuffdiff2 that requires a unique quantification method, Cufflinks [ 18].
At first, we visually check the resulting alignment, and count the number of (manifestly) correct and wrong occurrences.
To estimate the evolutionary distance between two sequences, we first compute a pairwise alignment and count the number of all nucleotide pair types in the alignment.
We focused on the top three hits from each alignment and counted each category for comparison using an in-house Perl script.
During the process we keep track of the inliers rate within the set C ab, as well as the time required by each technique to determine their best correspondence triplet within C ab. Once the alignments are terminated, we visually inspect the alignment outcome and count the number of errors for each technique, reported in Table 1.
The module miRNA identification" includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting.
A common workflow for micro-RNA sequencing (miRNA-seq) analysis includes adapter removal, sequence alignment, and read counting.
The pipeline in this module is categorized into "Raw data reading", "Adapter removal", "Sequence alignment", and "Reads counting" as a GUI-based step by step approach.
Aligning the sequences and counting the nucleotides at each position in the alignment provides a count matrix similar to those found in databases as TRANSFAC [1] and JASPAR [2].
Finally, any remaining A at the end of the read was removed prior alignment to the reference genome and counting.
