User: Tori
Tori • 90
- Reputation:
- 90
- Status:
- Trusted
- Location:
- Finland
- Last seen:
- 1 year, 9 months ago
- Joined:
- 5 years ago
- Email:
- b*****@live.com
Posts by Tori
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... I have following two IRanges objects query and ref. I would like to get overlap in number of basepairs.
> ref
chr start end
1 1 120 190
2 1 910 1050
3 1 1100 1140
4 1 2550 2650
5 2 50 100
> query
chr start end
1 1 101 173 ...
written 22 months ago by
Tori • 90
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... What if `df` has not only chr7 in first column? ...
written 2.8 years ago by
Tori • 90
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... Thank you very much! ...
written 2.8 years ago by
Tori • 90
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... I have methylation data which looks like this for example.
chr start end meth
chr7 31441 31441 0.16542433
chr7 31467 31467 0.93508003
chr7 50060 50060 0.38091076
chr7 50097 50097 0.31270269
chr7 50147 50147 0.39961491
chr7 50158 50158 0.01449239
chr ...
written 2.8 years ago by
Tori • 90
• updated
2.8 years ago by
andrew.j.skelton73 ♦ 5.9k
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... I have used Methylkit, RnBeads and RadMeth for analysing RRBS data, but after diving into greater detail of the result files of these methods DM regions with high p-value/qvalue does not make sense. Those statistically significant (high p-value/qvalue) DM regions do not seem significant in biologic ...
written 2.8 years ago by
Tori • 90
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... I am working on RRBS data. Someone suggested me to use M-values for the calculation of differential methylation. In my understanding beta-values/m-values are used to measure methylation level in array based method. In sequencing data we get single base pair resolution methylation level after methyla ...
written 2.8 years ago by
Tori • 90
• updated
2.8 years ago by
Devon Ryan ♦ 93k
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... How can I get table like following in R for hg38?
RefseqID Symbol Description EntrezID
NM_000014 A2M alpha-2-macroglobulin 2
NM_000015 NAT2 N-acetyltransferase 2 (arylamine N-acetyltransferase) 10
NM_000016 ACADM acyl-CoA dehydrogenase, C-4 to C-12 straight chain 34
NM_000017 AC ...
written 3.0 years ago by
Tori • 90
• updated
3.0 years ago by
WouterDeCoster ♦ 42k
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... I have samples from Whole Genome Bisulfite Sequencing. Lambda genome has been spiked-in. I calculate bisulfite conversion efficiency by mapping the data to lambda genome and calculate conversion efficiency using following equation.
Conversion efficiency = 100 - {no. of methylated Cs in CpG context/ ...
written 4.0 years ago by
Tori • 90
• updated
4.0 years ago by
Giovanni M Dall'Olio ♦ 26k
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... @Pierre Lindenbaum Thanks for your informative comment. So, PCR duplicates and optical duplicates can not be identified from BAM/SAM file because both have same flag 1024. If I plot x and y coordinates I can possibly see in the plot the location of the duplicates. If there are points very close to o ...
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... One of the reads from SAM file looks likes this
J00117:26:H3YC3BBXX:5:1224:28384:20918 419 chr1 12734 3 101M = 12855 222 TAGACAGTGAGTGGGAGTGGCGTCGCCCCTAGGGCTCTACGGGGCCGGCATCTCCTGTCTCCTGGAGAGGCTTCGATGCCCCTCCACACCCTCTTGATCTT AAFFFKKFKKKAFKKKKKKKKKKFKKKKKKKKKKKKFKKKKK ...
written 4.1 years ago by
Tori • 90
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For How can I calculate bisulfite conversion rate from RRBS data?
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For How to caclulate ChIP-Seq coverage?
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For Why 50bp Illumina run produces 51bp long sequencs?
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For Why 50bp Illumina run produces 51bp long sequencs?
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For How can I calculate bisulfite conversion rate from RRBS data?
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For How to caclulate ChIP-Seq coverage?
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