User: vm.higareda

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vm.higareda20
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Posts by vm.higareda

<prev • 33 results • page 1 of 4 • next >
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taxonomic classification with rna-seq data
... I have some single end RNA-seq data from Drosophila larvae and I would like to know what other microorganisms are present in my samples different to Drosophila. Do you have any recommendation? I have read that kraken can do taxonomic classification with RNA-seq and also IMSA+A. My RNA-seq librari ...
rnaseq kaiju taxonomy kraken imsa+a written 6 months ago by vm.higareda20
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Comment: C: Problem to run checkm.
... hello, Do you know how can interpret # genomes and # markers and # marker sets columns ? ...
written 8 months ago by vm.higareda20
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Comment: C: what is Kmer coverage
... How I can interpretate kmer coverage, what cov=243 mean? ...
written 10 months 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 10 months ago by vm.higareda20 • updated 10 months ago by Buffo1.8k
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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 18 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 21 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 2.3 years 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 2.4 years 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 2.4 years 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 2.4 years ago by vm.higareda20 • updated 2.4 years ago by h.mon30k

Latest awards to vm.higareda

Popular Question 18 months ago, created a question with more than 1,000 views. For counts in rna-seq cpm
Popular Question 18 months ago, created a question with more than 1,000 views. For Doubts about RNA-seq Cufflinks
Popular Question 18 months ago, created a question with more than 1,000 views. For Strand-option in hisat2
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Strand-option in hisat2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Using Hisat2 with strand specific bacteria sequences

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