I've been working with the FindNeighboringGenes tool and trying to limit the
neighborhood with the -b option. However it seems that genes even far outside
of this boundary are reported. Is that a bug in the software or am I using the
-b option in a wrong way?
So, far I've filtered the FNG file with the following awk command:
Hi
I've been working with the FindNeighboringGenes tool and trying to limit the
neighborhood with the -b option. However it seems that genes even far outside
of this boundary are reported. Is that a bug in the software or am I using the
-b option in a wrong way?
So, far I've filtered the FNG file with the following awk command:
awk 'FS="\t" { if($1 || ($4 && $4 <= 1000)) {print $0 }
}' FNG.xls
This removes all hits outside of the specified 1000bp boundary.
Thanks,
Deniz
Just wanted to show an example:
Example output for "-b 1500" option
chr10 374751 375342 0.0
204404 73 NM_212479 chr10 170642 285200 + 170642 Closest
204404 73 NM_006624 chr10 170642 290576 + 170642 Closest
chr10 1300976 1301497 1.0
105529 594 NR_015376 chr10 1195707 1200611 + 1195707 Closest
chr10 2386896 2387760 2.0
617611 74 NM_018702 chr10 1218072 1769717 - 1769717 Closest
If I'm looking at the right columns, these genes seem to have greater
distances than 1,500bp (e.g. 204,404bp).
Sorry, about the garbled message - here again:
Example output for "-b 1500" option
chr10 374751 375342 0.0
204404 73 NM_212479 chr10 170642 285200 + 170642 Closest
204404 73 NM_006624 chr10 170642 290576 + 170642 Closest
chr10 1300976 1301497 1.0
105529 594 NR_015376 chr10 1195707 1200611 + 1195707 Closest
chr10 2386896 2387760 2.0
617611 74 NM_018702 chr10 1218072 1769717 - 1769717 Closest
If I'm looking at the right columns, these genes seem to have greater
distances than 1,500bp (e.g. 204,404bp).