User: vm.higareda

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vm.higareda20
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Posts by vm.higareda

<prev • 31 results • page 1 of 4 • next >
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Comment: C: what is Kmer coverage
... How I can interpretate kmer coverage, what cov=243 mean? ...
written 7 weeks ago by vm.higareda20
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what is Kmer coverage
... I have been reading about kmer coverage value produced by DNA assemblers such as SPAdes or velvet, however I have not understand this concept. If i have the following SPAdes header: >NODE_3_length_237403_cov_243.207 cov=243, mean that 243 reads that were used to reconstruct the NODE3 contig ...
genome assembly sequence metagenome spades written 7 weeks ago by vm.higareda20 • updated 7 weeks ago by Buffo1.7k
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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 9 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 12 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 19 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 19 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 20 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 20 months ago by vm.higareda20 • updated 19 months ago by h.mon27k
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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 20 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 20 months ago by vm.higareda20

Latest awards to vm.higareda

Popular Question 9 months ago, created a question with more than 1,000 views. For counts in rna-seq cpm
Popular Question 9 months ago, created a question with more than 1,000 views. For Doubts about RNA-seq Cufflinks
Popular Question 9 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 Strand-option in hisat2
Popular Question 23 months ago, created a question with more than 1,000 views. For Using Hisat2 with strand specific bacteria sequences

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