User: v82masae

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v82masae100
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Posts by v82masae

<prev • 32 results • page 1 of 4 • next >
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Assesing Gene topology and connectivity
... Hi everyone in the Biostar community, I have been working on detecting Differentially Expressed (DE) genes from a RNAseq experiment between groups, and also assesing Differentially Disperse (DD) genes. Say, contrasting differences between means and between variances. I habe also calculated de Biolo ...
gene co-expresion topology rna-seq pathway written 13 days ago by v82masae100
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Answer: A: miRPara for novel miRNA discovery
... There are several tools out there, but in my experience, many of them are difficult or imposible to use. Some of them are not available any more or are web based so they are quite limited. miRDeep2 and Mirnovo are good options in my opinion, if you have smallRNAseq data. But their outputs can be qu ...
written 20 days ago by v82masae100
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Comment: C: Comparing novel miRNAs from miRDeep2
... Be carefull with removing quantification spots in your matrix. If same miRNAs have been quantified as mature or precursors or if some sequences quantified as different spots do really belong to the same transcript, the values in quantification matrix will be squeued and not representative of the rea ...
written 23 days ago by v82masae100
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Comment: C: STAR or Bowtie for small RNA seq?
... This would be quite expected in smallRNA-seq data after trimming sequencing adaptors and filtering low quality reads. ...
written 23 days ago by v82masae100
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Answer: A: STAR or Bowtie for small RNA seq?
... We get pretty decent alignment rates and accurate results with Bowtie and following specifications: bowtie -n 1 -l 10 -m 100 -k 1 --best --strata ...
written 23 days ago by v82masae100 • updated 23 days ago by ATpoint13k
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Answer: A: Comparing novel miRNAs from miRDeep2
... As far as I know, there is no easy way to do this. You could try to track where are these reads comming from in the genome alignment, and merge those clustered in the same region. mirDeep2 software does miRNA prediction considering each group of technical repeats as a single batch. The prediction p ...
written 23 days ago by v82masae100
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Answer: A: novel miRNA identification from sequence
... You could try a pipeline we recently developed in our team. Paper is still not published though. https://github.com/emarmolsanchez/eMIRNA ...
written 26 days ago by v82masae100
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RTqPCR Differential Expression with multivariate linnear models
... Hello everyone, So I have some data from RTqPCR experiment in different samples meassuring a number of genes (80-90). I have pre-processed de raw Ct data, correcting for efficiency, normalizing with reference genes with NormFinder and geNorm selected genes, averaging technical replicates and calcul ...
R limma linnear model written 3 months ago by v82masae100 • updated 3 months ago by Kevin Blighe37k
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Comment: C: VCF sample fields output
... I looked at the header and indeed it is refering to the PID and PGT fields. I have been looking about the meaning of this, related to physical phasing. From what I have understood, this applies for consecutive variants or near variants. I do not understand what are the implications of that, as I al ...
written 9 months ago by v82masae100
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VCF sample fields output
... Hi, I am analysing some SNPs in a VCF, and I have found some mutation of interest, but, I would like to know what this output in the samples fields mean. The two SNPs I am interested in are these: 1 270574995 . T C 8523.06 PASS AC=64;AF=0.889;AN=72;DP=333;FS=0.000;MQ=60.00;set=Intersect ...
vcf sample snp written 9 months ago by v82masae100 • updated 6 months ago by Biostar ♦♦ 20

Latest awards to v82masae

Popular Question 12 weeks ago, created a question with more than 1,000 views. For miRNA-mRNA expression correlation
Popular Question 8 months ago, created a question with more than 1,000 views. For Trimming adapters from miRNA-seq
Popular Question 9 months ago, created a question with more than 1,000 views. For Using limma for Differential Expression test
Popular Question 10 months ago, created a question with more than 1,000 views. For Using limma for Differential Expression test
Popular Question 14 months ago, created a question with more than 1,000 views. For Using limma for Differential Expression test
Popular Question 14 months ago, created a question with more than 1,000 views. For miRNA-mRNA expression correlation
Popular Question 14 months ago, created a question with more than 1,000 views. For Difference between CPM and RPM for RNA-seq reada quantification

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