User: pinky_pinkpinky

Reputation:
30
Status:
New User
Location:
India
Last seen:
5 months, 1 week ago
Joined:
3 years, 11 months ago
Email:
p**************@yahoo.co.in

Posts by pinky_pinkpinky

<prev • 38 results • page 1 of 4 • next >
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Tools that can be used to assembly GBS data
... Dear Users, 1. Can any one suggest some tools that can be used to perform assembly with GBS data (75*1) chemistry. 2. Any tools to perform hybrid assembly (Illumina PE and GBS SE) reads Many thanks in advance Thanks Pinky ...
assembly written 5 months ago by pinky_pinkpinky30
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Tools to identify the non-coding RNAs
... Dear Users, Can anyone recommend some tools that can identify all the non-coding RNAs in a genome. Thank You, ...
genome written 10 months ago by pinky_pinkpinky30 • updated 10 months ago by Michael Dondrup44k
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Annotation of Microorganisms
... Dear Users, I would like to know whether there is any database which provides the annotation of microorganisms related to their shape and metabolism. Thanks ...
sequencing written 18 months ago by pinky_pinkpinky30 • updated 18 months ago by natasha.sernova2.9k
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Homer known motif analysis
... Dear Users, I am intetested in identification of known motifs for my peaks generated using homer. I used homer for peak calling as well as motif generation. I got both the known and de novo motifs.But most of my required motifs are available in knownmotif.txt file.and known.motifs contains only the ...
chip-seq written 2.1 years ago by pinky_pinkpinky30
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Queries related to homer
... Dear users, I would. Like to know whether Homer does fold change w.r.t local tag count or clonal or input in log scale or linear scale.?? ...
chip-seq written 2.4 years ago by pinky_pinkpinky30
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Answer: A: Doubts related to MACS tool
... Thank You for your explanation. I would like to go one step back and would like get few more inputs. 1. You discussed about sample normalization using SPMR option. Is it supposed to be done separately for input and IP or  following the below mentioned script takes care of it ? callpeak -t treate ...
written 2.4 years ago by pinky_pinkpinky30
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Comment: C: Doubts related to MACS tool
... Dear Pierre, Thank You for your explanation. I would like to go one step back and would like get few more inputs. 1. You discussed about sample normalization using SPMR option. Is it supposed to be done separately for input and IP or  following the below mentioned script takes care of it ? call ...
written 2.4 years ago by pinky_pinkpinky30
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Annotation bug using HOMER
... Dear Users, I am getting the below mentioned issue while executing annotatePeaks.pl using HOMER. readline() on closed filehandle IN at /data/ngs/projects/Abhi/HOMER/bin/parseGTF.pl line 77. readline() on closed filehandle IN at /data/ngs/projects/Abhi/HOMER/bin/parseGTF.pl line 77.     Prioritizin ...
chip-seq written 2.5 years ago by pinky_pinkpinky30
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Answer: A: Doubts related to MACS tool
... Thanks Ian. I am not so confident with macs2 version. I have few fundamental doubts. It will be great if you can clarify them. 1. In macs2 output file NA_peaks.xlsx, what does pileup means? Does NA_peaks.xlsx gives only the enriched regions in treated sample? In manual it says , its the pileup he ...
written 2.5 years ago by pinky_pinkpinky30
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Doubts related to MACS tool
... Dear Users, I have few doubts using MACS2 Peakcalling 1. macs2 callpeak -t chip.bedgraph -c input.bedgraph --outdir Input_test -B --nomodel --SPMR This step generates a control lambda.bdg file and a treated pileup bdg file.   As per my understanding --SPMR normalizes the dataset to 1M reads . So ...
chip-seq written 2.6 years ago by pinky_pinkpinky30

Latest awards to pinky_pinkpinky

Popular Question 10 months ago, created a question with more than 1,000 views. For Query related to generating plots from HOMER output
Popular Question 10 months ago, created a question with more than 1,000 views. For Application of Hi-C
Popular Question 10 months ago, created a question with more than 1,000 views. For Peak plots using R
Popular Question 18 months ago, created a question with more than 1,000 views. For Doubts related to MACS tool
Popular Question 18 months ago, created a question with more than 1,000 views. For Application of Hi-C
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Issues related to HOMER
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Doubt related terms used in HOMER for ChipSeq Analysis
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Peak plots using R
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Chip-Seq GO analysis

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