User: RT

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RT330
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Posts by RT

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Answer: A: Open positions at the Center for Molecular Oncology, MSKCC, New York
... Hi Cyriac, Since this post is modified two days ago, I am wondering if these positions are still open? Thanks, Reetu ...
written 5 days ago by RT330
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Data mining for 300 genes from GEO
... Hi All, I have a gene list of ~ 300 genes. I want to get from GEO all the high-throughput expression studies for these genes. I can write a R script to make this search with GEOsearch package. But I guess the package only allows for geneid/name based search. I was wondering if there is a way to sea ...
geo written 12 months ago by RT330 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: Select top differentially expressed genes based on both p-value and fold-change
... so what is the best way to select top genes? As I said, I was suggested to consider both p-values and fold-change and use rankproduct for this. Rankproduct is used for identification of DEGs. I am not sure how to apply it to foldchange and pvalue. Any other ideas of combining pval and fc for seelc ...
written 13 months ago by RT330
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Select top differentially expressed genes based on both p-value and fold-change
... I always selected top differentially expressed genes based on p-values (DESeq2 for differential-expr analysis). Just recently, someone suggested me to use both p-value and fold change to select top genes. I am little confused as p-values already take fold-change into consideration. Can someone shed ...
differential-expression deseq2 rna-seq written 13 months ago by RT330 • updated 13 months ago by Santosh Anand3.5k
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meme-suite: How does FIMO works?
... Dear All, I am new to motif identification area. From a set of sequences (~200), I want to search for a known motif and filter out sequences where the motif does not exist. My motif is 8bp long. A simple python search gave me too many random hits. Someone quickly suggested to me to use meme-tools a ...
meme-suite motif identification fimo written 14 months ago by RT330 • updated 13 months ago by Santosh Anand3.5k
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pybedtools change fasta headers
... I am using pybedtools to get promoter sequences for my genes of interest. I am almost done with the script. But I would also like to include gene names in the fasta headers. By default, it only include corrdinates in fasta headers. Below is my script: >coords=Chr1 1000 2000 forward 1 + >a ...
python pybedtools written 14 months ago by RT330
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Chip-seq on pooled replicates
... Dear All, Can someone please help me to understand why for ChIP-seq we should not merge the biological replicates before peak calling. I read in several papers, peaks calling is done on individual replicates. I am struggling to understand this. Ideally if I merge replicates I should have more power ...
chip-seq pooled replicates written 15 months ago by RT330 • updated 15 months ago by EagleEye5.1k
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Comment: C: Macs2 failed for pooled samples
... I am very confused now. I actually started following IDR pipeline. Does not it recommend to run macs2 on both individual replicates and pooled replicates? https://sites.google.com/site/anshulkundaje/projects/idr ...
written 15 months ago by RT330
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macs2 warnings unknown sequencing problem
... Hi All, I have chipseq single-end reads of length 130 bp. From macs2 output I got the warning 'Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!'. Can it be because macs2 is not estimating the fragment length correctly ...
chipseq macs2 single end data written 15 months ago by RT330
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Macs2 failed for pooled samples
... Dear All, I am new to ChIP analysis. I have 3 replicates for ChIP samples and 2 for control samples. I am using macs2 for peak calling. It was all going well until I called peaks on pooled replicates. MACS2 command: macs2 callpeak -t chipdata_pooled.tagAlign.gz -c mocksamples.tagAlign.gz -f B ...
macs2 chip-seq written 15 months ago by RT330 • updated 15 months ago by EagleEye5.1k

Latest awards to RT

Great Question 4 months ago, created a question with more than 5,000 views. For How to extract all the mapped reads from bwa output
Great Question 4 months ago, created a question with more than 5,000 views. For How To Correctly Classify Gene Families?
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Popular Question 4 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 9 months ago, created a question with more than 5,000 views. For How To Correctly Classify Gene Families?
Popular Question 9 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 9 months ago, created a question with more than 1,000 views. For Using ML tree or bootstrapped tree
Popular Question 9 months ago, created a question with more than 1,000 views. For Mapping coordinates from gff file to individual gene
Popular Question 9 months ago, created a question with more than 1,000 views. For loss of function prediction
Popular Question 11 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 11 months ago, created a question with more than 1,000 views. For Using ML tree or bootstrapped tree
Student 11 months ago, asked a question with at least 3 up-votes. For Limma Package For Differential Expression Between Control And Stress
Popular Question 12 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 13 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
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Popular Question 16 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 17 months ago, created a question with more than 5,000 views. For Limma Package For Differential Expression Between Control And Stress
Popular Question 17 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 18 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
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