User: chaudharyc61

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chaudharyc6120
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India
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1 week, 1 day ago
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Posts by chaudharyc61

<prev • 26 results • page 1 of 3 • next >
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How to smooth methylation data
... Hello Everyone I have a TAB delimited file having details as Chr Window_start Window_end Mutant_Meth_score Wild_Meth_score log2(Wild_Meth_score/Wild_Meth_score) I want to smooth the Log2 value so that i can easily use it to plot in R using plot function. Can anyon ...
bisulfite-seq analysis written 8 days ago by chaudharyc6120 • updated 5 days ago by Kevin Blighe54k
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Extracting Multiple Mapped reads from Bismark output
... Hello everyone Bismark aligner gives a a report like : - Final Alignment report Sequences analysed in total: 10000 Number of alignments with a unique best hit from the different alignments: 6703 Mapping efficiency: 67% Sequences with no alignments under any conditi ...
bs-seq data alignment written 5 weeks ago by chaudharyc6120 • updated 4 weeks ago by onestop_data160
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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 5 weeks ago by chaudharyc6120
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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 5 weeks ago by chaudharyc6120
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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 5 weeks ago by chaudharyc6120 • updated 5 weeks ago by Devon Ryan94k
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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 6 weeks ago by chaudharyc6120 • updated 6 weeks ago by bernatgel2.4k
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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 6 weeks ago by chaudharyc6120 • updated 6 weeks ago by ATpoint29k
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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 6 weeks ago by chaudharyc6120 • updated 6 weeks ago by ATpoint29k
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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 8 weeks ago by chaudharyc6120 • updated 8 weeks ago by ATpoint29k
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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 6 months ago by chaudharyc6120

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