User: v82masae

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v82masae140
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Posts by v82masae

<prev • 34 results • page 1 of 4 • next >
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Modify BED with poliregions
... I have a somewhat tricky BED file format, which I should convert to a classic BED format so as I can properly use it for further steps: I have this unconventional BED format: 1 12349 12398 + 1 23523 23578 - 1 23550;23570;23590 23640;23689;23652 + 1 43533 43569 ...
bed bash awk written 4 months ago by v82masae140 • updated 4 months ago by Pierre Lindenbaum121k
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Answer: A: miRNA differential expression
... Unless your targeted organism has very poor sequenced genome, I would strongly suggest to map your smallRNA-seq to the reference genome, and then count aligned reads by using miRNA GFF or GTF positions. About what software to use for Differential Expression. EdgeR or DESeq2 ar both good options, an ...
written 4 months ago by v82masae140
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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 5 months ago by v82masae140
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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 5 months ago by v82masae140
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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 5 months ago by v82masae140
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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 5 months ago by v82masae140
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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 5 months ago by v82masae140 • updated 5 months ago by ATpoint19k
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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 5 months ago by v82masae140
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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 5 months ago by v82masae140
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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 8 months ago by v82masae140 • updated 8 months ago by Kevin Blighe45k

Latest awards to v82masae

Popular Question 7 months ago, created a question with more than 1,000 views. For miRNA-mRNA expression correlation
Popular Question 13 months ago, created a question with more than 1,000 views. For Trimming adapters from miRNA-seq
Popular Question 14 months ago, created a question with more than 1,000 views. For Using limma for Differential Expression test
Popular Question 15 months ago, created a question with more than 1,000 views. For Using limma for Differential Expression test
Popular Question 19 months ago, created a question with more than 1,000 views. For Using limma for Differential Expression test
Popular Question 19 months ago, created a question with more than 1,000 views. For miRNA-mRNA expression correlation
Popular Question 19 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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