User: chaudharyc61

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Posts by chaudharyc61

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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 4 days ago by chaudharyc610
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DiffBind package showing warnings and unable to analyse my data
... Hello everyone I am using DiffBind Bio-conductor for differential binding analysis. I have four replicates of same experiment so the Condition column is same for all the replicates, while getting the contrast in R (**i.e My_data <- dba.contrat(My_data, categories = DBA_CONDITION)** ) I am gettin ...
diffbind chip-seq written 4 days ago by chaudharyc610 • updated 2 days ago by Rory Stark510
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idr command line error
... Hello everyone I am using Irreproducible Discovery Rate (idr), which is successfully installed in my Ubuntu 18.04 LTS. after sorting the narrowPeak files by p.value, I'm trying to get idr report but this is the message i'm getting on terminal : Traceback (most recent call last): File "/us ...
idr chip-seq written 10 days ago by chaudharyc610 • updated 10 days ago by lakhujanivijay4.2k
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Handling replicates in Chip-seq
... Hello everyone, I have three replicates for my ChIP-seq data, i did peak calling using MACS2, now i was thinking to get the common peaks from all the replicates which in my sense can be called as significance peaks. Now i have some questions 1. Which tool or algorithm should i use to do that and ...
replicates chip-seq written 11 days ago by chaudharyc610 • updated 11 days ago by ATpoint19k
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Comment: C: Bedtools Intersect related
... I havn't used any strictness and this is the command i used bedtools intersect -a A.bed -b B.bed > Inter.bed bedtools intersect -a Inter.bed -b C.bed > Final.bed Using this my logic is the common peaks from A and B i can get common peak from C ...
written 11 days ago by chaudharyc610
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Comment: C: Bedtools Intersect related
... The thing is i have different replicates of same experiment and to get significant peaks i'm using this approach as if same peak is coming in all the three files it has more chances to be called as significant peak. In that way i have to find same peaks through out three files and manually it is no ...
written 11 days ago by chaudharyc610
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Bedtools Intersect related
... Hello everyone Let's say i have three files A.bed, B.bed and C.bed which are having coordinates of peaks. Using bed-tools intersect i got common peaks or i guess those are common. My question is: Is there any other way using bed-tools by which i can find the exact common peaks from all the three f ...
bedtools chip-seq tool bedfiles written 11 days ago by chaudharyc610 • updated 11 days ago by 2nelly160
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Comment: C: MACS2 result of FDR
... While peak calling did you change the default p-value ? ...
written 17 days ago by chaudharyc610
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MACS2 result of FDR
... Hello everyone As one of the output file of macs2 is in excel form which tells -log10(q-value) which is the FDR (False Discover Rate) I wan to ask whether the highest q-value is reliable or the lowest as every peak has its own -log10(q-value) In other words if -log10(q-value) is 10.08 of one peak is ...
false discovery rate macs2 chip-seq q-value written 4 weeks ago by chaudharyc610 • updated 4 weeks ago by genomax69k
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Comment: C: Peak calling using spp package
... While calling peak it is creating problem I am using spp package for peak calling and it is not giving binding characterstics ...
written 4 weeks ago by chaudharyc610

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