Running BLAT with maximum sensitivity

nohup /home/shah/local_progs/blat_dir/blat -fine -repMatch=1000000 -minIdentity=100 /home/shah/drosophila_annotations/dmel3_apr_2006/dmel3_apr_2006.fasta agilent_dm2_probe_sequences_5_215453.fasta agilent_dm2_probe_sequences_5_215453.psl &

explanation :

-fine
-repMatch=1000000 - number when tiles are considered overused
-minIdentity=100 - pick identical matches

e.g. for mapping probes to the reference genomes.

Installing R package tar.gz

use

R CMD INSTALL pkg.tar.gz


or within R session

install.packages("pkg.tar.gz", type="source", repos=NULL)

Running xMAN for Affy probe mapping

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

Generating a Affymatrix "tpmap" file for TiMAT

R Code that uses the Bioconductor module Affxparser.

Note: The code has a bug and in normal circumstances returns an error

> writeTpmap(filename="Dm_tiling2_MR_v01.tpmap", bpmaplist=bpmapr)
> Error in as.vector(y) : argument "y" is missing, with no default

The "y" can be fixed as follows

> y <- readBpmap("Dm_tiling2_MR_v01.bpmap")
> writeTpmap(filename="Dm_tiling2_MR_v01.tpmap", bpmaplist='y', verbose = as.integer(0))

This seems to work but doesn't print anything into the tpmap file due to some "sequence skipping".

I will try the Affymatrix windows based program next.