User: kashiff007

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kashiff00770
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Posts by kashiff007

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Reporting methylation of both Cs and Gs, or only Cs
... Thank for your clear answer. I want to know why I have to consider both methylation level (from C and subsequent G) for the analysis. Let's say I want look at the methylation level inside the promoter of a gene, since genes are defined in the strand specific does it not make sense to take only Cs (f ...
written 20 days ago by kashiff00770
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Reporting methylation of both Cs and Gs, or only Cs
... Hi All, I just started working with methylation (WGBS) data. I have used Bismark and it generated the methylation of Cs and consecutive Gs. I am guessing this Gs methylation is from Cs from other strand (please correct me if I am wrong). My question is should I consider both while reporting the met ...
next-gen methylation bs-seq bismark sequencing written 20 days ago by kashiff00770 • updated 20 days ago by Devon Ryan91k
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Answer: A: plot error x y length difference
... Try this code. It should solve your problem data <- read.csv("~/Desktop/my_data.csv", header=TRUE) dim(data) rnames <- data[,1] # assign labels in column 1 to "rnames" mat_data <- data.matrix(data[,2:ncol(data)]) # transform column 2-5 into a mat ...
written 7 weeks ago by kashiff00770 • updated 7 weeks ago by RamRS24k
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Comment: C: plot error x y length difference
... Have you checked the first few lines of "m3" matrix. what is your head(m3) output? ...
written 7 weeks ago by kashiff00770
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Comment: C: macs14 replicates treatment and final wiggle peak files
... Thanks @geek_y for such detail explanation. Al thought have you ever encounter the following error while running the macs14. "error occurred: Invalid variableStep wig file format in line starting with "variableStep chrom=chr3 span=10" what could be the reason for this? Thanks ...
written 3 months ago by kashiff00770
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Comment: C: macs14 replicates treatment and final wiggle peak files
... By control I mean input here. Can I use treated wig/bw directly to see my enrichment of do I have to do manual subtraction of treated wig - control (input) wig file? "I would get the bigwigs with -log10(p-value), to show enrichment over inputs." will this file be generated or do I have to use som ...
written 3 months ago by kashiff00770
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macs14 replicates treatment and final wiggle peak files
... Hi, I have few quick question regarding macs14? - How one can treat the replicates? Do I have to run separately and then take average from the final peaks or is there any way to include it in one run? - macs14 generates two wig files under "--single-profile" option; one for control and one fo ...
replicates chip-seq macs14 wig-file written 3 months ago by kashiff00770 • updated 3 months ago by geek_y9.8k
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Faster way to run macs14
... Hi, Is there any way to run macs14 with multicore processor (or multi-thread)? The objective is to run it faster. Thanks ...
chip-seq multithread macs14 multicore written 3 months ago by kashiff00770
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Merge MNase-seq bam files from replicates.
... I am working with MNase-seq data. I have few replicates from samples. For the analysis, I have to work on distogram (histograms of distances between mapped reads’ start positions aligning in opposing orientation), phasogram (histograms of distances between mapped reads’ start positions aligning in t ...
replicates mnase-seq merge next-gen bam-files written 6 months ago by kashiff00770
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Answer: A: How to distinguish if a gene is a paralogue or an isoform?
... According to the basic definition isoforms are coming from same gene, so their location should be same in the genome. At least, in most cases TSS and TTS are usually same for all transcript. While paralogs are the result of duplication so their position differ from the original gene. Technically par ...
written 6 months ago by kashiff00770

Latest awards to kashiff007

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: plot error x y length difference
Scholar 7 weeks ago, created an answer that has been accepted. For A: Combining two columns in a tab-delimited file where there is a zero in one
Popular Question 14 months ago, created a question with more than 1,000 views. For How to generate pair-wise alignments for all the orthologous gene pairs at once?
Popular Question 14 months ago, created a question with more than 1,000 views. For Cufflinks generating multi-transcripts
Scholar 2.0 years ago, created an answer that has been accepted. For A: Combining two columns in a tab-delimited file where there is a zero in one

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