Nimblegen Probes

aleferna · 08-06-2010, 06:14 AM

#chr10 NimbleScan TEST1/Ms-4C/gDNA/MseI 112111377 112111427 0.08 . . ;chr10P112111377;1
#chr10 NimbleScan TEST1/Ms-4C/gDNA/MseI 112111477 112111527 0.31 . . ;chr10P112111477;1
#chr10 NimbleScan TEST1/Ms-4C/gDNA/MseI 112111577 112111627 -0.19 . . ;chr10P112111577;1

#CHR11 NimbleScan ESC/Mb-4C1/gDNA/Mbo1 11570417 11570467 1.26 + . CHR11:11425301-12332192;CHR1100P011570417;1
#CHR11 NimbleScan ESC/Mb-4C1/gDNA/Mbo1 11570469 11570519 0.91 + . CHR11:11425301-12332192;CHR1100P011570469;1
#CHR11 NimbleScan ESC/Mb-4C1/gDNA/Mbo1 11570521 11570571 1.67 + . CHR11:11425301-12332192;CHR1100P011570521;1

I'm going through some old nimblegen tiling array gff files and they have 2 types of lines. The first show a single position on the genome (;chr10P112111577;1) and the second show a range (CHR11:11425301-12332192;CHR1100P011570469;1). I understand the second type, but what is the first?? I looked at the ndf file and it doesn't explain it.

cjfields · 08-10-2010, 12:25 PM

In the first example, the name can't be reporting a single position. It's more likely the specific probe ID. The number might represent the count; compare it to a recent set of GFF3 output I have:

Code:

##gff-version	3
AARF01000001	NimbleScan	data_371701C03_HX1_U01_Apis_532:BLOCK1	256	305	867.89	.	.	seq_id=AARF01000001:1-883;probe_id=AARF01000001FS000000256;count=1

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08-06-2010, 06:14 AM	#1
aleferna Senior Member Location: sweden Join Date: Sep 2009 Posts: 121	Nimblegen Probes #chr10 NimbleScan TEST1/Ms-4C/gDNA/MseI 112111377 112111427 0.08 . . ;chr10P112111377;1 #chr10 NimbleScan TEST1/Ms-4C/gDNA/MseI 112111477 112111527 0.31 . . ;chr10P112111477;1 #chr10 NimbleScan TEST1/Ms-4C/gDNA/MseI 112111577 112111627 -0.19 . . ;chr10P112111577;1 #CHR11 NimbleScan ESC/Mb-4C1/gDNA/Mbo1 11570417 11570467 1.26 + . CHR11:11425301-12332192;CHR1100P011570417;1 #CHR11 NimbleScan ESC/Mb-4C1/gDNA/Mbo1 11570469 11570519 0.91 + . CHR11:11425301-12332192;CHR1100P011570469;1 #CHR11 NimbleScan ESC/Mb-4C1/gDNA/Mbo1 11570521 11570571 1.67 + . CHR11:11425301-12332192;CHR1100P011570521;1 I'm going through some old nimblegen tiling array gff files and they have 2 types of lines. The first show a single position on the genome (;chr10P112111577;1) and the second show a range (CHR11:11425301-12332192;CHR1100P011570469;1). I understand the second type, but what is the first?? I looked at the ndf file and it doesn't explain it.

08-10-2010, 12:25 PM	#2
cjfields Junior Member Location: Champaign, IL, USA Join Date: Sep 2009 Posts: 6	In the first example, the name can't be reporting a single position. It's more likely the specific probe ID. The number might represent the count; compare it to a recent set of GFF3 output I have: Code: ##gff-version 3 AARF01000001 NimbleScan data_371701C03_HX1_U01_Apis_532:BLOCK1 256 305 867.89 . . seq_id=AARF01000001:1-883;probe_id=AARF01000001FS000000256;count=1