User: Andrés Ribone

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Posts by Andrés Ribone

<prev • 15 results • page 1 of 2 • next >
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Comment: C: freebayes not reading the chunks of regions file
... Where are you specifying the region? ...
written 6 weeks ago by Andrés Ribone0
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Comment: C: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc
... Hi! Thanks for the quick reply!!! I'm using the varianceStabilizingTransformation() function from DESeq2, but I'm applying it to my raw counts matrix *without* using the DESeq() function. I'm doing this because I wasn't sure what model should I input to the function nor how exactly that could affec ...
written 7 weeks ago by Andrés Ribone0
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Variance Stabilizing Transformation on RNAseqs coming from different studies
... Hi! I have a lot of public RNA-seqs from different experiments and genotypes sharing similar conditions/tissues. I want to build gene co-expressions networks out of them. I did all the process to get the raw counts of every sample. I removed the samples with low counts (I rejected samples with les ...
wgcna rna-seq vst written 7 weeks ago by Andrés Ribone0 • updated 7 weeks ago by Kevin Blighe69k
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Comment: C: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc
... Hi Kevin, I'm dealing with something similar, and wanted to check some things: I have a lot of public RNA-seqs from different experiments and genotypes sharing similar conditions/tissues. I want to build co-expressions networks out of them. I did all the process to get the raw counts of every sa ...
written 7 weeks ago by Andrés Ribone0
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Issue with Salmon and Deseq2 with paired-end and single-end reads libraries
... Hi, I have an issue regarding using Salmon and Deseq2 with mixed (paired-end and single-end) read libraries. My libraries were originally paired end, but I quality-trimmed them, resulting in a lot of single-end reads that I don't want to throw away. I want to use Salmon to quantify expression. B ...
rnaseq tximport deseq2 salmon written 11 months ago by Andrés Ribone0
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featureCounts log: "WARNING contig is not found in the provided genome file!"
... Hi, I'm working with sunflower (Helianthus annuus) RNAseq data. I mapped my read to the XRQ genome, and then tried to count reads using featureCounts. gff=/path/to/file/HanXRQr1.0-20151230-EGN-r1.2.gff3 genome=/path/to/file/HanXRQr1.0-20151230.fa bamdir=/path/to/bams/ featureCoun ...
featurecounts subread rna-seq written 11 months ago by Andrés Ribone0 • updated 11 months ago by dbpzdbpz140
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Population / Reference bias in GATK BQSR BaseRecalibrator?
... Hi, I work in sunflower (H. annuus) transcriptomics. I'm trying to genotype a big amount of RNAseqs samples from wild accessions (coming from distant places). I have used the reference genome for alignment and resulted a not-so-terrible alignment rate (mean=92%,min=81%,max=95%). Now, for the BQSR s ...
population bias gatk bqsr non model organism written 14 months ago by Andrés Ribone0
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Comment: C: DESeq2: why the independent filtering threshold would come back as NULL please?
... Watch out the final dot! Thank you! ...
written 2.6 years ago by Andrés Ribone0
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Comment: C: How do I find input arguments (RGPU, RGLB, etc) for AddOrReplaceReadGroups
... Hey, about the differing barcodes: there must be a barcode that outnumber the rest for many magnitude orders, that is the cannon; the rest should differ only in one base. ...
written 2.6 years ago by Andrés Ribone0
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Cmscan multithreading issue
... Hi I'm working in de novo transcriptome assembling from RNA-seq data. Right now I'm using Rfam cmscan to annotate 58808 contigs I got (N50=800). I'm working in a debian virtual machine in a cluster with 16 cores and 32 Gb ram. Setting cmscan to use all the cores I have available when annotating the ...
transcriptome assembly infernal rfam cmscan written 3.2 years ago by Andrés Ribone0

Latest awards to Andrés Ribone

Popular Question 7 months ago, created a question with more than 1,000 views. For De novo transcriptome assembly of low amount of Illumina reads with MIRA
Popular Question 10 months ago, created a question with more than 1,000 views. For Bowtie2 orientation mapping question
Popular Question 23 months ago, created a question with more than 1,000 views. For Fast visualisation of BLAST search hits' annotations

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