User: chaudharyc61

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chaudharyc6140
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India
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2 days, 12 hours ago
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1 year, 8 months ago
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Posts by chaudharyc61

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Does read length of RNA seq affects the results ?
... Yes, both data groups are sequenced at different timepoints. ...
written 9 days ago by chaudharyc6140
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Does read length of RNA seq affects the results ?
... Hello everyone As my question in my title says "Does read length of RNA seq affects the results ?" So I ahve a wild type of 75 BPs paired end data and mutant is of 150 BPs paired end. After mapping does that affects the DEGs ? Thank you Chandan kumar ...
next-gen deseq2 rna-seq written 10 days ago by chaudharyc6140 • updated 10 days ago by ponganta50
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Plotting telomere to centromere data pf a genome
... Hello everyone I am trying to plot my peaks (in case of ChIP-seq) and methylation data ( in case of BS-Seq) in a format of telomere to centromere representation. Example of the picture is fig1D from [PNAS paper ][1] [1]: https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.pnas.org%2Fcont ...
R next-gen chip-seq written 6 weeks ago by chaudharyc6140
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Replicates in Bisulfite data
... Hello everyone I am working with plant BS-Seq data. I have six datasets, three mutant and three wild type. all the datasets are generated with different samples and experiments. So the replicates are of different experiments,same tissue. My question is should i take the unique positions of Cytosin ...
methylation bisulfite-seq written 3 months ago by chaudharyc6140 • updated 3 months ago by dariober11k
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To get correlation of different ChIP-seq samples
... Hello everyone I wanted to get the correlation of different ChIP data samples. I have made 10kb windows and got z-scored log2 values of each window to plot the data. I was wondering, to get the correlation, should i use z-scored log2 values or just log2 values or direct values which i got per win ...
genome next-gen chip-seq written 6 months ago by chaudharyc6140 • updated 6 months ago by Shalu Jhanwar480
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annotation parameter in ChIPQC
... Hey everyone I am trying to take another txDB object as annotation in ChIPQC function, but the function is creating an issue. > Error in getAnnotation(annotation, AllChr = chromosomes) : Unsupported annotation:TAIR10 This is my code >library(ChIPQC) >library(TxDb.Athaliana.BioMart. ...
chip-seq chipqc written 7 months ago by chaudharyc6140 • updated 6 months ago by Biostar ♦♦ 20
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Getting position of features of chromosomes
... Hello everyone, I wanted to know the approximate range of start and end positions of telomere, p-arm, centromere and q-arm of each chromosome of Arabidopsis thaliana. Is there any tool or website using which i can get this information somehow ? Thank you Chandan kumar ...
genome telomere centromere written 7 months ago by chaudharyc6140
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Comment: C: Positive Negative Strand
... Hey I have a question, so if i want to do a motif analysis of a set of gene ids i should consider the positive and negative strand orientation too, for negative strand i should take end+500 positions and fro positive strand start+500 position, right? ...
written 7 months ago by chaudharyc6140
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error in reading bam file in methylKit
... Hello everyone, I am working on methyl-seq data. I have used bismark for alignment and the alignment file is sorted and indexed BAM file. And alignment is local alignment, but when i'm trying to open the file in methylKit , i'm getting error of > Error in methCall(read1 = location, type = "bam" ...
bisulphite methylkit written 8 months ago by chaudharyc6140
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Comment: C: About Mapping Efficiency of Bisulfite aligners
... yes because i tried extracting reads with higher MAPQ values using > samtools view -b -q 5 Aligned_reads.sam -o Quality5.bam And i got zero reads in the output file. ...
written 10 months ago by chaudharyc6140

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Popular Question 12 weeks ago, created a question with more than 1,000 views. For Handling replicates in Chip-seq

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