User: samsara

gravatar for samsara
samsara570
Reputation:
570
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Trusted
Location:
The Earth
Last seen:
4 years, 9 months ago
Joined:
6 years, 8 months ago
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b********@gmail.com

I am sorry, I don't know anything about myself.

Posts by samsara

<prev • 71 results • page 1 of 8 • next >
9
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1
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2.3k
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9 follow
1
answer
How Much Is Too Much For 5 Prime End Methylation Rate In Rrbs Data ?
... I have RRBS fastq files. I used Bismark to perform methylation call. After methylation call I got M-bias plot shown below. The methylation rate of first three bases of 5 prime end is quite high. The actual methylation count and rate of first four position is shown below. My questions are: Is t ...
next-gen written 5.0 years ago by samsara570
2
votes
1
answer
2.2k
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1
answer
Are There Any Alternatives To Methylkit For Methylation Call ?
... I have RRBS data. I tried to find differentially methylated promoter region using methylKit, but it reported promoter regions that does not have any base methylated. The result does not seem reliable. Are there any alternative to methylKit for methylation call ? ...
methylation written 5.1 years ago by samsara570 • updated 5.1 years ago by Devon Ryan88k
0
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3
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11k
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3
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Comment: C: Promoter Or Enhancer Regions Bed Format
... how can i extract promoters in galaxy once i load bed from from UCSC ? ...
written 5.1 years ago by samsara570
2
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1
answer
2.4k
views
1
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Is It Possible To Get Features Count Directly From Tophat?
... I have been using HTSeq to count number of reads per feature for RNA-Seq. I am just wondering, Is it possible to get counts through Tophat by providing GTF file without using HTSeq? ...
tophat2 written 5.1 years ago by samsara570
0
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2
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3.2k
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2
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Comment: C: Are There Any Tools For Finding Methylation Status Of Promoter Region?
... it really helped. One more query, where can i find mm10 promoter sequences bed file ? ...
written 5.2 years ago by samsara570
0
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2
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3.2k
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2
answers
Comment: C: Are There Any Tools For Finding Methylation Status Of Promoter Region?
... Before methylKit, i need to perform methylation call. Which is mostly used methylation call software? ...
written 5.2 years ago by samsara570
9
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2
answers
3.2k
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5 follow
2
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Are There Any Tools For Finding Methylation Status Of Promoter Region?
... I have have data from RRBS (Reduced representation bisulfite sequencing). I have already mapped fastq files using Bismark. I have never worked with RRBS data, therefore got little lost. What are the tools options for finding methylation status of promoter region? Are there any widely used pipelines ...
promoter methylation written 5.2 years ago by samsara570 • updated 5.2 years ago by Ian5.3k
0
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4
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12k
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4
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Comment: C: How Can I Find Out Unknown Illumina Barcode.
... I run FastQC to check over-represented sequences, before posting this question, but FastQC did not give any over-represented sequences. ...
written 5.2 years ago by samsara570
17
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4
answers
12k
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11 follow
4
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How Can I Find Out Unknown Illumina Barcode.
... I have fastq file with undetermined reads from Illumina HiSeq. The reads in fastq file contains illumina barcode. I do now know what barcode has been used in the lab and there is no way i could find it out. Is it possible to find it out from the fastq file I received. Are there any tools that show m ...
reads illumina fastq hiseq written 5.2 years ago by samsara570 • updated 2.1 years ago by elgart0
0
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1
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4.1k
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1
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How Can I Create Similarity Matrix From Gene Expression And Rnaseq Data?
... I have gene expression (log2 lowess normalized) of different samples as follows genes sample1 sample2 sample3 sample4 g1 -0.25 -0.91275 -0.641 0.37 g2 1.3245 -2.126 7.495 -1.151 g3 0.31775 0.731 -1.151 0.182 ... I have rnaSeq (gene quanification dat ...
rnaseq written 5.3 years ago by samsara570 • updated 2.1 years ago by Biostar ♦♦ 20

Latest awards to samsara

Student 5.0 years ago, asked a question with at least 3 up-votes. For How Much Is Too Much For 5 Prime End Methylation Rate In Rrbs Data ?
Supporter 5.0 years ago, voted at least 25 times.
Student 5.2 years ago, asked a question with at least 3 up-votes. For How Can I Find Out Unknown Illumina Barcode.
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Bowtie Alignment And Low Percentage Of Mapped Reads

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