User: vm.higareda

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vm.higareda20
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2 years, 9 months ago
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Posts by vm.higareda

<prev • 29 results • page 1 of 3 • next >
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kallisto with reference genome
... Is it correct to use a reference genome to build a kallisto index and use this index to run kallisto quant?. I have genome of a bacteria, extracted the complete sequence of the genes and used this multi fasta file to build the index ...
kallisto rna-seq written 4 months ago by vm.higareda20
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HTseq-counts not counting correctly?
... Hello I am doing a DE analysis of Drosophila, after mapping my fasq file to Drosophila genome with hisat2. I am using htseq-count with the gtf file to get the count table. In the count table, I have the identifier corresponding to 28S rRNA and 18S rRNA, but it has ZERO counts, that can not be poss ...
htseq drosophila rna-seq written 7 months ago by vm.higareda20
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Comment: C: counts in rna-seq cpm
... I did differential expression analysis with edgeR and Deseq, but I would like to compare one gene along different treatments not only pairwise comparison. I am confused how to do that ...
written 14 months ago by vm.higareda20
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Comment: C: counts in ran-seq cpm
... I would like to take a look of counts of one specific gene along different treatments so I think that could be better do it using the cpm not the raw counts. What do you think? The idea is detect outlier counts in a specific gene not it all the treatment ...
written 15 months ago by vm.higareda20
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Comment: C: EdgeR (TMM): Samples with outlier but still show extremely low p-value and FDR
... But even if you see one replica is an outliers as in your example?¿ Did you trust in that gene? ...
written 15 months ago by vm.higareda20
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counts in rna-seq cpm
... hello I am conscious that there are different programs to detect differential expression in transcriptome data, but would be correct if I compare the cpm of the same gene between different treatments, only to have an idea about the variance betwen genes. I can use de cpm function of edgeR What ...
data transcriptomics rna-seq edger cpm written 15 months ago by vm.higareda20 • updated 15 months ago by h.mon25k
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Comment: A: EdgeR (TMM): Samples with outlier but still show extremely low p-value and FDR
... Hello Did you resolve your problem? I have similar a behaviour with use edgeR. If i have one outlier in one of my four biological replicates the program takes it as DE gene. I don't understand why this happen, but seem to be common am thinking to changue to deseq2 ...
written 15 months ago by vm.higareda20
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detecting antisense transcripts
... Hello I am analyzing a single end strand specific (dUTP), transcriptome of *D.melanogaster*. I have already mapped and counted my sequences using: hisat2 --rna-strandness R htseq-count -f bam -s reverse Now, I would like to detect antisense transcripts How could do that? Thanks ...
strand rna illumina antisense rna-seq written 15 months ago by vm.higareda20
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Comment: C: edgeR understanding statistics
... Thank you for your response, the old post and paper are really interesting. This is an old problem. I don't not understand why edgeR developments do not solved this problem. ...
written 19 months ago by vm.higareda20
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Comment: C: edgeR understanding statistics
... Yes it was useful, thank you for your answer. I am still confused why this kind of programs do not take in account outlier replicates ...
written 19 months ago by vm.higareda20

Latest awards to vm.higareda

Popular Question 14 months ago, created a question with more than 1,000 views. For Strand-option in hisat2
Popular Question 19 months ago, created a question with more than 1,000 views. For Using Hisat2 with strand specific bacteria sequences

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