Noi/NOTES/2012-4-27: Difference between revisions

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== Check chromosome and coordinate of CpG and SNP derived from mapping on TRiton and from Robert's ASM pipeline ==
== Check chromosome and coordinate of CpG and SNP derived from mapping by bisReadMapperSE19Triton and from Robert's ASM pipeline ==
* Triton mapping
* 509557 GK0005-001.hg19.BED.txt
sort GK0005-001.hg19.BED.txt > sorted_chrpos_GK0005-001.hg19.BED.txt
509557 sorted_chrpos_GK0005-001.hg19.BED.txt
track name="GK0005-001_hg19" description="Methylation level" visibility=2 useScore=1 itemRgb="On"
chr10 100017297 100017298 0.983 58 + 100017297 100017298 210,0,0
chr10 100017304 100017305 0.930 57 + 100017304 100017305 210,0,0
chr10 100017325 100017326 1.000 58 + 100017325 100017326 210,0,0
chr10 100017333 100017334 0.964 55 + 100017333 100017334 210,0,0
chr10 100029179 100029180 0.951 41 + 100029179 100029180 210,0,0
chr10 100029247 100029248 0.450 40 + 100029247 100029248 90,150,0
chr10 100029342 100029343 0.026 39 + 100029342 100029343 0,240,0
chr10 100029476 100029477 0.897 58 + 100029476 100029477 210,0,0
chr10 100029482 100029483 0.276 58 + 100029482 100029483 60,180,0
* Robert's pipeline
488563 CpGMethFreq.GK0005001.bed
sort CpGMethFreq.GK0005001.bed > sorted_CpGMethFreq.GK0005001.bed
488563 sorted_CpGMethFreq.GK0005001.bed
track name="GK0005001 CpG MF" description="GK0005001 CpG Methylation Frequency" visibility="dense" useScore=1 itemRgb="On"
chr10 100017297 100017298 0.982 57 + 100017297 100017298 210,0,0
chr10 100017304 100017305 0.929 56 + 100017304 100017305 210,0,0
chr10 100017325 100017326 0.999 57 + 100017325 100017326 210,0,0
chr10 100017333 100017334 0.965 57 + 100017333 100017334 210,0,0
chr10 100029179 100029180 0.950 40 + 100029179 100029180 210,0,0
chr10 100029247 100029248 0.450 40 + 100029247 100029248 90,150,0
chr10 100029342 100029343 0.026 39 + 100029342 100029343 0,240,0
chr10 100029476 100029477 0.897 58 + 100029476 100029477 210,0,0
chr10 100029482 100029483 0.276 58 + 100029482 100029483 60,180,0
* The number of called CpG by Robert's pipeline was lower than bisReadMapperSE19Triton. This is possible that Robert's pipeline is more stringent than bisReadMapperSE19Triton, so the number of called CpG was lower. However the chromosome positions, CpG coordinates and methylation frequency were consistent.
== Check the CpG coordination in ASM output file ==
* To check if the CpG coordinate from ASM analysis is on start or end position.
** CpG coordinates in BED file mapped by bisReadMapperSE19Triton are on the end position
* File's description:
(9) MFASMAnalysisPValues.$expname.$asmtesttype.txt
1st field is the SNP coordinate,
2nd field is the SNP call,
3rd field is the strandedness of the SNP call (ss - single strand ds - double strand),
4th field is the strand of the SNP call,
5th field is the type of calculation (a number stands for the coordinate of a specific CpG. Stable and stable average are defined above).
6th field shows the difference in methylation frequency values between CpGs on SNP bases 1 and 2
7th field is the p-value associated with the observed allele specific differential methylation values.
8th and 9th are the number of C's and T's associated with SNP base1, respectively.
Fields 10 and 11 are the number of C's and T's associated with SNP base2, respectively.
 
MFASMAnalysisPValues.GK0005001.cpg.txt
3:173374 AG ss - '''173345''' -0.0262626262626262 0.783557175124665 36 8 38 7
CpGMethFreq.GK0005001.bed
chr3    173344  '''173345'''  0.831  89      +      173344  173345  180,60,0
MFASMAnalysisPValues.GK0005001.cpg.txt
20:62405863 CG ss - '''62405854 ''' 0.153846153846154 0.402328024619046 22 4 9 4
CpGMethFreq.GK0005001.bed
chr20  62405853        '''62405854'''        0.810  42      +      62405853        62405854        180,60,0
* This means that the CpG coordinates from ASM analysis are on the end position as the CpG in methylFreqMatrix as well

Revision as of 18:13, 27 April 2012

Check chromosome and coordinate of CpG and SNP derived from mapping by bisReadMapperSE19Triton and from Robert's ASM pipeline

  • Triton mapping
  • 509557 GK0005-001.hg19.BED.txt
sort GK0005-001.hg19.BED.txt > sorted_chrpos_GK0005-001.hg19.BED.txt
509557 sorted_chrpos_GK0005-001.hg19.BED.txt
track name="GK0005-001_hg19" description="Methylation level" visibility=2 useScore=1 itemRgb="On"
chr10	100017297	100017298	0.983	58	+	100017297	100017298	210,0,0
chr10	100017304	100017305	0.930	57	+	100017304	100017305	210,0,0
chr10	100017325	100017326	1.000	58	+	100017325	100017326	210,0,0
chr10	100017333	100017334	0.964	55	+	100017333	100017334	210,0,0
chr10	100029179	100029180	0.951	41	+	100029179	100029180	210,0,0
chr10	100029247	100029248	0.450	40	+	100029247	100029248	90,150,0
chr10	100029342	100029343	0.026	39	+	100029342	100029343	0,240,0
chr10	100029476	100029477	0.897	58	+	100029476	100029477	210,0,0
chr10	100029482	100029483	0.276	58	+	100029482	100029483	60,180,0
  • Robert's pipeline
488563 CpGMethFreq.GK0005001.bed
sort CpGMethFreq.GK0005001.bed > sorted_CpGMethFreq.GK0005001.bed
488563 sorted_CpGMethFreq.GK0005001.bed
track name="GK0005001 CpG MF" description="GK0005001 CpG Methylation Frequency" visibility="dense" useScore=1 itemRgb="On"
chr10	100017297	100017298	0.982	57	+	100017297	100017298	210,0,0
chr10	100017304	100017305	0.929	56	+	100017304	100017305	210,0,0
chr10	100017325	100017326	0.999	57	+	100017325	100017326	210,0,0
chr10	100017333	100017334	0.965	57	+	100017333	100017334	210,0,0
chr10	100029179	100029180	0.950	40	+	100029179	100029180	210,0,0
chr10	100029247	100029248	0.450	40	+	100029247	100029248	90,150,0
chr10	100029342	100029343	0.026	39	+	100029342	100029343	0,240,0
chr10	100029476	100029477	0.897	58	+	100029476	100029477	210,0,0
chr10	100029482	100029483	0.276	58	+	100029482	100029483	60,180,0
  • The number of called CpG by Robert's pipeline was lower than bisReadMapperSE19Triton. This is possible that Robert's pipeline is more stringent than bisReadMapperSE19Triton, so the number of called CpG was lower. However the chromosome positions, CpG coordinates and methylation frequency were consistent.

Check the CpG coordination in ASM output file

  • To check if the CpG coordinate from ASM analysis is on start or end position.
    • CpG coordinates in BED file mapped by bisReadMapperSE19Triton are on the end position
  • File's description:
(9) MFASMAnalysisPValues.$expname.$asmtesttype.txt 
1st field is the SNP coordinate,
2nd field is the SNP call, 
3rd field is the strandedness of the SNP call (ss - single strand ds - double strand), 
4th field is the strand of the SNP call,
5th field is the type of calculation (a number stands for the coordinate of a specific CpG. Stable and stable average are defined above). 
6th field shows the difference in methylation frequency values between CpGs on SNP bases 1 and 2
7th field is the p-value associated with the observed allele specific differential methylation values. 
8th and 9th are the number of C's and T's associated with SNP base1, respectively. 
Fields 10 and 11 are the number of C's and T's associated with SNP base2, respectively.
MFASMAnalysisPValues.GK0005001.cpg.txt 
3:173374	AG	ss	-	173345	-0.0262626262626262	0.783557175124665	36	8	38	7
CpGMethFreq.GK0005001.bed
chr3    173344  173345  0.831   89      +       173344  173345  180,60,0
MFASMAnalysisPValues.GK0005001.cpg.txt
20:62405863	CG	ss	-	62405854	 0.153846153846154	0.402328024619046	22	4	9	4
CpGMethFreq.GK0005001.bed
chr20   62405853        62405854        0.810   42      +       62405853        62405854        180,60,0
  • This means that the CpG coordinates from ASM analysis are on the end position as the CpG in methylFreqMatrix as well