User: chaudharyc61

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chaudharyc6130
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India
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1 month ago
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1 year, 6 months ago
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Posts by chaudharyc61

<prev • 34 results • page 2 of 4 • next >
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Comment: A: How does samtools markdup works?
... To use samtools markdup there's a set of commands i believe you should use. These are the commands, I used for my data. `samtools sort -n -o Sorted_names.bam -O BAM Alignment.bam` explanation: This command will sort your Alignment file based on the names of reads. `samtools fixmate -m Sorted_nam ...
written 10 months ago by chaudharyc6130
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Comment: C: About Mapping Efficiency of Bisulfite aligners
... Thank you so much for clearing my doubt. What do you mean by setting MAPQ while extracting methylation ??? ...
written 10 months ago by chaudharyc6130
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About Mapping Efficiency of Bisulfite aligners
... Hello Everyone I have mapped my own data from Arabidopsis meiocytes cells, with BS-seeker2 and bismark with both of modes (End-toEnd and local). The mapping efficiency is obviously different as BS-Seeker2 uses local alignment. My question is :- Is it okay to use local alignment for BS-seq data wi ...
methylation bs-seq written 10 months ago by chaudharyc6130 • updated 10 months ago by Devon Ryan97k
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Plotting CpG methylation
... Hello Everyone I am new to NGS and trying to plot a Genomic landscape having information of CpG methylation over adjacent 1000 bps width window data. My file looks like this: 1. chr1 0 1000 12.6 2. chr1 1000 2000 45.8 3. chr1 2000 3000 31.3 4. chr1 3000 4000 10.2 where the last column has valu ...
methylation written 10 months ago by chaudharyc6130 • updated 10 months ago by bernatgel2.7k
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Answer: A: What is P value and Padj value in DEGs ?
... As I understand, from your question, you need to read this , this article will help you understnad the logic behind it. [Why, When and How to Adjust Your P Values?][1] All the best [1]: https://www.ncbi.nlm.nih.gov/pubmed/30124010 ...
written 10 months ago by chaudharyc6130 • updated 10 months ago by ATpoint41k
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About Mapping Efficiency of Bisulfite aligners
... Hello everyone, I am working with my own Bisulfite data generated as single-end reads. So, when i'm using Bs-seeker2 i'm getting a mapping efficiency of approx 75-80% but at the same time if i'm using Bismark or BSMap aligner the mapping efficiency get down by 30%. I can't understand the why it is ...
bisulfite-sequencing alignment written 10 months ago by chaudharyc6130 • updated 10 months ago by ATpoint41k
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Identifying differential methylation regions
... Hello Everyone, I am working with our own data of methyl-seq. I have made a file which has format : Chr Start_window End_window Difference_bw_methylation_of_two_genptypes This file is an overlapping file which means 0 to 300bps and 200bps to 500bps (100bps overlapping) Now i want to make r ...
methyl-seq written 11 months ago by chaudharyc6130 • updated 11 months ago by ATpoint41k
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ChIP-seq Input correlation
... Hello Everyone I have done multiBamSummary on my ChIP-seq data, and i found that the data has correlation with my Input is 0.98 which is almost similar, What i mean is my treatment data file and Input file is showing correlation 0.98 My question is should i go for downstream analysis or not ? T ...
chip-seq correlation written 15 months ago by chaudharyc6130
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Comment: C: Error in peak calling using SPP package
... Please Check your data whether it's single-end or paired-end ?? spp package works with single-end data only... ...
written 15 months ago by chaudharyc6130
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Answer: C: idr command line error
... I downloaded CRAN version of idr (R-package) and used in RStudio from the URL: > https://cran.r-project.org/web/packages/idr/ ...
written 16 months ago by chaudharyc6130

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