User: chaudharyc61

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chaudharyc6110
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Posts by chaudharyc61

<prev • 17 results • page 1 of 2 • next >
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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 3 months ago by chaudharyc6110
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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 3 months ago by chaudharyc6110
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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 months ago by chaudharyc6110
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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 months ago by chaudharyc6110 • updated 4 months ago by Rory Stark550
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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 4 months ago by chaudharyc6110 • updated 4 months ago by lakhujanivijay4.5k
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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 4 months ago by chaudharyc6110 • updated 4 months ago by ATpoint26k
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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 4 months ago by chaudharyc6110
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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 4 months ago by chaudharyc6110
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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 4 months ago by chaudharyc6110 • updated 4 months ago by 2nelly170
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Comment: C: MACS2 result of FDR
... While peak calling did you change the default p-value ? ...
written 4 months ago by chaudharyc6110

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