runBlast: Run BLAST for small RNA sequences
In timjeske/DEUS: Differential expression of unique sequences

Description Usage Arguments Value

This function takes a vector of sequences in FASTA style as input and applies BLAST running on a local blast database. By default, the parameters are configured for blasting small RNA sequences of strand-specific RNA-seq experiments with 100% identity over the whole query sequence.

1 2	runBlast(blast_exec, blast_db, ncores, sig_sequences, strand = "plus", identity = 100, dust = "no", soft_masking = "false")

`blast_exec`	Path to your installation of the 'blastn' binary
`blast_db`	Path to your local BLAST database
`ncores`	Number of cores used by BLAST
`sig_sequences`	Vector of sequences in FASTA style generated by the sequencesAsFasta
`strand`	Query strand orientation to search against database. By default 'plus', assuming underlying strand-specific RNA-seq experiments.
`identity`	Identity cutoff applied for filtering BLAST results. By default 100%, to find only exact matches over the whole length of the query sequence.
`dust`	The parameter specifies whether low complexity filtering is applied to the query sequence. By default 'no', to prevent false-negative annotations of sequences of interest.
`soft_masking`	The parameter specifies whether low complexity filter is applied to the database. By default 'no', to prevent false-negative annotations of sequences of interest.

Each row of the resulting data frame corresponds to a BLAST hit including the columns 'qseqid', 'qlen', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue' and 'bitscore'.

timjeske/DEUS documentation built on June 6, 2019, 12:59 p.m.