User: RT

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RT290
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Posts by RT

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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 3 days ago by RT290
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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 4 weeks ago by RT290
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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 4 weeks ago by RT290 • updated 4 weeks ago by Santosh Anand2.2k
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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 9 weeks ago by RT290 • updated 4 weeks ago by Santosh Anand2.2k
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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 11 weeks ago by RT290
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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 3 months ago by RT290 • updated 3 months ago by EagleEye3.9k
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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 3 months ago by RT290
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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 3 months ago by RT290
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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 3 months ago by RT290 • updated 3 months ago by EagleEye3.9k
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samtools flag 1548
... Hi all, Just a quick question- can somebody please explain to me what is the meaning of 1548 in the following samtools command: samtools view -b -F 1548 Thanks, RT ...
bitwise flags samtools written 3 months ago by RT290 • updated 3 months ago by Pierre Lindenbaum94k

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