The phrase "aligned file" is correct and usable in written English.
It can be used in contexts related to data organization, formatting, or ensuring that files are properly arranged or formatted for specific purposes.
Example: "Before submitting the report, make sure to save it as an aligned file to ensure proper formatting."
Alternatives: "formatted file" or "organized file".
Then, Skylign (Wheeler et al. 2014) was used to generate sequence logo after inputting the aligned file.
Sequence similarity was calculated based on the aligned file of mature tRNA sequences (.aln).aln
Known and predicted α-isopropylmalate synthase sequences were downloaded from GenBank and genome sequencing centers, the sequences were aligned (File S1), and maximum likelihood was used to infer phylogenetic relationships.
This aligned file is indexed with SAMtools to yield the processed aligned file.
Each aligned file was tagged with a file-specific identifier using "RAPGAP_alignment_tagger.pl" and the aligned files were concatenated together.
Phylogenetic analysis of the aligned file was performed by using MEGA5 (www.megasoftware.net) with the neighbor-joining method.
Triplicates from ATAC-seq data were merged to produce unified aligned files and which were then transformed to heat maps using deepTools2 (version 2.2.4) with a 10 kb window59.
For comparison, cufflinks was run using the multiple aligned files option simultaneously on all aligned files (bam format) of the ENCODE cell lines.
For technical replicates, Eland aligned files or BAM files were merged and processed as described in Fenouil et al. (2012).
Thus, approximately 27.4% of our raw data aligns to our targeted regions in our processed aligned files, yielding an average fold enrichment of 413 (±10.8).
Briefly, aligned files were processed with SAMtools and subsequently VarScan (V.2.2) 13 for the detection of A to G (positive strand) or T to C (negative strand) substitutions.
