Reads in ELAND output file, returning 5'-end tag coordinates and number of mismatches associated with each mapped tag.
read.eland.tags(filename,
read.tag.names = F,
fix.chromosome.names = T,
max.eland.tag.length = -1,
extended=F,
multi = F)ELAND output file
Whether the tag names should be read in
Whether to remove ".fa" from the end of the sequence names
Specifies max length of the tag sequence considered by ELAND. This needs to be specified if the tags are longer than the sequences considred by ELAND during alignment.
Whether the file is written out in "extended" format provided in GA pipeline 1.0.
Whether the file is written in "multi" format, showing multiple alignments of the reads
A vector of 5' tag coordinates, with negative values corresponding to tags mapped to the negative strand.
Number of mismatches
Tag names, if read.tag.names was set