| PackageDescription | integrated RNA-Seq read analysis
CRAC is a tool to analyze High Throughput Sequencing (HTS) data in
comparison to a reference genome. It is intended for transcriptomic
and genomic sequencing reads. More precisely, with transcriptomic
reads as input, it predicts point mutations, indels, splice junction,
and chimeric RNAs (ie, non colinear splice junctions). CRAC can also
output positions and nature of sequence error that it detects in the
reads. CRAC uses a genome index. This index must be computed before
running the read analysis. For this sake, use the command "crac-index"
on your genome files. You can then process the reads using the command
crac. See the man page of CRAC (help file) by typing "man crac". CRAC
requires large amount of main memory on your computer. For processing
against the Human genome, say 50 million reads of 100 nucleotide each,
CRAC requires about 40 gigabytes of main memory. Check whether the
system of your computing server is equipped with sufficient amount of
memory before launching an analysis. |