User: Nitin Narwade

gravatar for Nitin Narwade
Nitin Narwade440
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440
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Location:
India
Last seen:
1 week ago
Joined:
3 years, 6 months ago
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n***************@gmail.com

Posts by Nitin Narwade

<prev • 97 results • page 1 of 10 • next >
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Comment: C: Empty output when use HOMER annotatePeak.pl
... You need to add a homer bin directory in your executable path (ex.: .bashrc). Follow the instructions given on the homer installation page. Look for subsection 4. under **Installing the basic HOMER software** section on the homer installation page. Thanks. ...
written 3 months ago by Nitin Narwade440
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Comment: C: How to perform a gene set analysis in edgeR?
... What are the IDs (First column in the edgeR input file) you're using to run edgeR.? ...
written 3 months ago by Nitin Narwade440
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Comment: C: RNA-SeQC v1.1.8 transcript_id attribute was not found
... Though I haven't used RNA-SeQC ever, by looking at the reported error `The required transcript_id attribute was not found on line 1 ....` it seems the tool is looking for the transcript_id attribute and your input `.gtf` file is having gene records at first line (probably that could be the master ...
written 3 months ago by Nitin Narwade440
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Comment: C: Control concatenation order in a fasta file
... In your code, `opendir` will get the directory content in sorted order. As you mentioned if the names of the files are exactly the same as `fie1_OTIB.fasta, file2_OTIA.fasta, file3_OTSS.fasta, file4_OTLS` then you will get output as your expecting but if the file names are without `file(number)_` p ...
written 3 months ago by Nitin Narwade440
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Comment: C: Plot read density across a normalized gene model for its each exon/intron length
... BTW, where and how did you get this representation? ...
written 3 months ago by Nitin Narwade440
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Comment: C: pick one sequence per locus
... It will be really difficult to understand what you're asking without sample input and possible sample output. Thanks. ...
written 3 months ago by Nitin Narwade440
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Comment: C: Differential binding with SICER/epic2
... Can you post the sample output of epic-df tool (FC values)? ...
written 3 months ago by Nitin Narwade440
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Comment: C: Correlation between gene of interest and gene list (module)
... Subset the TCGA expression for your gene of interest and then find out the correlation. df <- read.table(file = "TCGA.expression.data.tsv", header = T, sep = "\t", row.names = 1) cor(t(df[c("A", "D", "E", "F", "H"),])) ...
written 3 months ago by Nitin Narwade440
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Comment: C: Differential binding with SICER/epic2
... Both the scatter plots seem the same to me. I think there is a slight variation in p-value and it is obvious because of sample comparison (A_vs_B and B_vs_A). ...
written 3 months ago by Nitin Narwade440
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Comment: C: Differential binding with SICER/epic2
... I think It should depend on your experimental condition. I mean, It is just **treatment over control** comparison. Now if you consider WT as your normal / control condition then you should use **FC WT vs KO**, which will be the differential binding of KO over WT. If you check the results of FC KO ...
written 3 months ago by Nitin Narwade440

Latest awards to Nitin Narwade

Popular Question 12 months ago, created a question with more than 1,000 views. For how to filter ChIP-Seq peaks called by MACS based on the measurements?
Scholar 16 months ago, created an answer that has been accepted. For A: about bioperl script for extracting sequences from a fasta file(get orf output f
Scholar 18 months ago, created an answer that has been accepted. For A: about bioperl script for extracting sequences from a fasta file(get orf output f
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: about bioperl script for extracting sequences from a fasta file(get orf output f

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