User: herman.pappoe.45

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Posts by herman.pappoe.45

<prev • 13 results • page 1 of 2 • next >
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Comment: C: How to run rlog from Deseq2 in R on HTseq counts from RNAseq data
... So I have tried creating a design matrix but I am not entirely sure I have designed correctly for the data I have: time sample day0.x time1 sample1 day2.x time2 sample2 day5.x time3 sample3 day14.x time4 sample4 day0.y time1 sample5 day2.y time2 sample6 day5. ...
written 2.9 years ago by herman.pappoe.4510
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How to run rlog from Deseq2 in R on HTseq counts from RNAseq data
... Hi all, I have RNA-Seq time-series data generated by HTseq counts. There are sort of 2 replicates. The First replicate has 4 time point samples(day0,2,5,14), while the Second has 5 time point samples(day0,2,5,15,30). The data was loaded as a read.table matrix in R. The following is the script use ...
R htseq counts rlog deseq2 rna-seq written 2.9 years ago by herman.pappoe.4510 • updated 2.9 years ago by informatics bot560
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Comment: C: Normalization Procedure For The Rna-Seq Data Based On Counts
... Can you use rlog function in R to normalize HT-seq counts? The issue is that I have loaded my data matrix consisting of counts generated from HTseq for RNA-Seq time-series data. There are sort of 2 replicates. First replicate has 4 time point samples(day0,2,5,14), while the Second has 5 time point ...
written 2.9 years ago by herman.pappoe.4510
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Answer: A: 【tophat】 RNA-seq mapping reference genome
... Hello I am experiencing the same issue as the OP. I have ***increased the memory*** as you have suggested. My command line looks like this: qsub -cwd -V -l ***num_proc=8,h_data=32G***,h_rt=24:00:00 -N day0_tophat -b y "module load tophat; module load bowtie2; module load samtools; tophat -g 1 ***- ...
written 2.9 years ago by herman.pappoe.4510
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Comment: C: Fast Qseq To Fastq Converter
... Hi Pablo, I was also interested in perhaps using the program you've made, unfortunately, it is completely missing from the link you provided. ...
written 3.0 years ago by herman.pappoe.4510
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Comment: C: Fast Qseq To Fastq Converter
... Hi Darked89, I am having difficulty compiling the converter with scons. I am new to Bioinformatics and I would extremely appreciate it, if you could possibly list the commands you used to: 1)install scons in the designated environment and 2)subsequently the commands necessary to compile qseq2fast ...
written 3.0 years ago by herman.pappoe.4510
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Answer: A: How to select top ranking genes with variance from a time point experiment usin
... This is what the excel file is like. By using the covariance function in excel for Day 0 and Day 2 for example, I get a single resulting value. I simply selected the covariance.s function and highlighted the cells for Day0 as the first array and the cells for Day 2 as the second array and clicked do ...
written 3.1 years ago by herman.pappoe.4510
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Comment: C: How to select top ranking genes with variance from a time point experiment usin
... Yes  I can, which output are you referring to?   ...
written 3.1 years ago by herman.pappoe.4510
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How to select top ranking genes with variance from a time point experiment using R or Excel
... Hello everyone, I have RNA seq data of human cardiomyocyte samples collected at 5 different time points of the development of the cells (i.e. Day0, Day2, Day5, Day15, Day 30). The model is hence a directed differentiation system. I am using a file with normalized RPM counts for each transcript ID f ...
variance R rna-seq time-point excel written 3.1 years ago by herman.pappoe.4510
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Comment: C: extract only geneID and gene symbol from GTF file
... I know perhaps I should make a separate question for this, but please bare with me. What command-line approach can be implemented to for example select only gene_id column in gtf file? I am aware of awk command, but as a newbie I have no clue how I would put this command together. Preferably a one-l ...
written 3.2 years ago by herman.pappoe.4510

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