xMAN commandline

Here is the xMAN how to from Tao Liu


Text formatted bpmap may not be processed by MAT directly. You need to convert your text bpmap to a so-called 'plainseq' format. Please type 'xMAN' without any argument to see the usage for detail.

And here is the commandline used to generate bpmap for fruitfly:

xMAN -f bpmap -i Dm_tiling2_MR_v01.bpmap -s Dm_tiling2_MR_v01.stderr -o Dm_tiling2_MR_v01_dm3 --nro=Dm_tiling2_MR_v01_dm3_all.NR --maxSeqCopy=10 --ProbeResolution=35 dm3/all/*.fa

The input file is a binary bpmap downloaded from affy website. And I put all the genome sequence files in dm3/all/ directory. Please remember to add '-nro' argument. After the run, the file 'Dm_tiling2_MR_v01_dm3_all.NR.bpmap' can be used by MAT.

Making MAT RepeatLib

Download the repeat_mask.txt, simple_repeat.txt and segment_dups.txt from UCSC

and run

python Rep.py -m repeat_mask.txt simple_repeat.txt segment_dups.txt

The Rep.py is available at the MAT lib subdirectory of the MAT install.

For the genomes like Drosophila melanogaster, for which UCSC doesn't provide Segment Duplication file. The repeat library can be generated by

1) remove all the instances of usage of "segdup" from Rep.py file
2) remove the original Rep.py and Rep.pyc files form MAT compile.
3) Recompile MAT.

RepeatLib and the modified Rep.py files are also available on request from me.
parantu dot shah at gmail dot com