User: catherine12243

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Posts by catherine12243

<prev • 35 results • page 1 of 4 • next >
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linear regression on EPICmethylation data
... Hi all, I have a 2*2 study design where each subject got measured pre-exposed and post-exposed for low-exposure and high-exposure group. so it is 10 patients x 2 groups x 2 (pre & post)= 40 samples of methylation data. and i want to run linear model to see the differential methylation associate ...
R methylation edger written 2.3 years ago by catherine12243120 • updated 2.3 years ago by theobroma221.1k
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Comment: C: methylation probe numbers
... Yes, I was using that function. RGset<-read.metharray.exp(base = NULL, targets = samplesheet_epic, recursive = T,force = TRUE) I got confused with those versions as well, but your answer is very helpful and at least I know I was using the correct parameter. ...
written 2.4 years ago by catherine12243120
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methylation probe numbers
... I was wondering what determines probe number of your sample? I'm processing methylationEPIC data using minfi `preprocessRaw`, and it gives me 865859 features/probes. But in the quality notice from Illumina, it states 866895 probes. why there's difference? Thank you in advance ...
assembly next-gen methylationepic written 2.4 years ago by catherine12243120 • updated 2.4 years ago by andrew.j.skelton735.8k
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extract only geneID and gene symbol from GTF file
... Hi Everyone, I want to get geneID(gene_id) and its associated gene symbol(gene_name) from a gtf file into a file that can be read into R. my gtf file looks like this:      chr1    HAVANA  gene    3073253 3074322 .       +       .       gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUSG000001 ...
genome gtf python written 4.5 years ago by catherine12243120 • updated 14 months ago by Minstein130
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macs2 output-narrowpeak file understanding?
... I used MACS2 to call peaks, and one file with NAME_peaks.narrowPeak, 5th column is "integer score for display" according to the documentation. But I don't understand what that means and how did they get the numbers. Also when I put it into IGV, peaks showed in color difference, and each peak may hav ...
macs chip-seq written 4.6 years ago by catherine12243120 • updated 3.7 years ago by Ulduz20
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how to know the strands of MACS call peaks
... I want to create a heatmap for chip-seq data by Homer program http://homer.salk.edu/homer/ngs/quantification.html the command is like this: annotatePeaks.pl <peak file> <genome> -size <#> -hist <#> -ghist -d <tag directory 1> [tag directory2] ... > <output matri ...
macs homer chip-seq written 4.6 years ago by catherine12243120 • updated 4.6 years ago by Jennifer Hillman Jackson390
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Comment: C: How Can I Convert Bam/Sam To Wiggle
... I got error Traceback (most recent call last): File "bam_wiggle.py", line 31, in from bcbio.pipeline.config_utils import load_config, get_program ImportError: No module named bcbio.pipeline.config_utils Is there anything else required other than `pysam` and `wigToBigWig`? Tha ...
written 4.6 years ago by catherine12243120 • updated 12 months ago by RamRS24k
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Answer: A: How Can I Convert Bam/Sam To Wiggle
... The python script showed above doesn't work well for me. So I would recommend samtools mpileup as well. ...
written 4.6 years ago by catherine12243120
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Comment: C: merge large amount of fastq files into a single one
... οh yeah! i was so stupid! ...
written 4.6 years ago by catherine12243120
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merge large amount of fastq files into a single one
... I have 30 small fastq files from same sample, and I want to merge it into one file. I know the command is  cat file1.fastq file2.fastq > bigfile.fastq but is there any short cut for doing it? It just looks silly to type 30 file names one by one... Thank you for any idea! ...
fastq chip-seq written 4.6 years ago by catherine12243120 • updated 4.6 years ago by Pierre Lindenbaum124k

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Popular Question 2.3 years ago, created a question with more than 1,000 views. For MAnorm error: unable to open files
Popular Question 2.4 years ago, created a question with more than 1,000 views. For MAnorm error: unable to open files
Great Question 3.7 years ago, created a question with more than 5,000 views. For merge large amount of fastq files into a single one
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Popular Question 3.7 years ago, created a question with more than 1,000 views. For MAnorm error: unable to open files
Popular Question 3.7 years ago, created a question with more than 1,000 views. For how to know the strands of MACS call peaks
Popular Question 3.7 years ago, created a question with more than 1,000 views. For merge large amount of fastq files into a single one
Popular Question 3.7 years ago, created a question with more than 1,000 views. For extract only geneID and gene symbol from GTF file
Popular Question 3.7 years ago, created a question with more than 1,000 views. For TSS file for D.melanogaster
Popular Question 3.7 years ago, created a question with more than 1,000 views. For macs2 output-narrowpeak file understanding?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For how to do vmatchPattern() for DNAStringSet [edited]
Popular Question 3.7 years ago, created a question with more than 1,000 views. For gene IDs not recognized by DAVID
Popular Question 3.7 years ago, created a question with more than 1,000 views. For cuffcompare error: cannot locate input file
Popular Question 3.7 years ago, created a question with more than 1,000 views. For normalize on chip-seq data
Student 3.7 years ago, asked a question with at least 3 up-votes. For how to know the strands of MACS call peaks
Student 3.7 years ago, asked a question with at least 3 up-votes. For merge large amount of fastq files into a single one
Popular Question 4.2 years ago, created a question with more than 1,000 views. For merge large amount of fastq files into a single one
Popular Question 4.2 years ago, created a question with more than 1,000 views. For normalize on chip-seq data

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