According to Drosophila Tiling 2.0R array design and library file description Affy tiling2.0R BPMAP file may contain probes that map to genomes multiple times, which may be derived from repeated gene families and other sequences that were not repeat masked.
Existence of probes that map to genomes multiple times lead to inflated p-values during the subsequent analysis and lead to false-positives. Also, remapping the probes to a newer genome assembly is desirable sometimes
Thus, it is important to remap the BPMAP to the genomes.
xMAN is available from Shirley Liu's lab.
Command line while running xMAN may look like
First try:
xMAN -f bpmap -i Dm_tiling2_MR_v01.bpmap -o Dm_tiling2_MR_v01_xman_nr.bpmap --nro=Dm_tiling2_MR_v01_xman_nro.bpmap --maxSeqCopy=10 chr2L.fa chr3L.fa chr2RHet.fa chr3RHet.fa chrUextra.fa chr4.fa chrX.fa chr2LHet.fa chr3LHet.fa chrM.fa chrXHet.fa chr2R.fa chr3R.fa chrU.fa chrYHet.fa
Subscribe to:
Post Comments (Atom)
No comments:
Post a Comment