User: rafaelsolersanblas

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Posts by rafaelsolersanblas

<prev • 13 results • page 1 of 2 • next >
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Chicken/Non canonical animal sequencing depth and read length
... Hi! Do you know what is the correct Illumina sequencing protocol to perform? We are between 50 bp Hiseq 2500 with a sequencing depth of 50M of reads, or NexSeq 75-150 bp read length with a sequencing depth of 30M. What is more important for non canonical organisms (like chicken and others) whom ...
chicken rna-seq sequencing written 3 months ago by rafaelsolersanblas30
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Why it is not use UMIs for RNA-seq?
... Hello, This is a theoretical question. Why scRNA seq data have their UMIs to later on eliminate the PCR bias, but in bulk RNA seq it has no UMIs?? I know that in scRNAseq the PCR contamination is bigger, and I know that you can use Picard, but doing it only by the coordinates I find it very risky, ...
scrna-seq umis rna-seq written 3 months ago by rafaelsolersanblas30 • updated 3 months ago by jperezboza20
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ATAC-seq quality filtering
... Hello, I am new with the ATAC-seq analysis. I am performing now the quality controls and I wanted to know if I am doing all the necessary steps. Also could be that I am filtering the data to much and losing information: > **Filtering mt reads and chloroplast** > > **Remove PCR duplicates ...
atac-seq written 3 months ago by rafaelsolersanblas30
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Comment: C: ATAC-seq problem with STAR - Multimapping reads
... Thank you!! I will test with Bowtie2 ...
written 3 months ago by rafaelsolersanblas30
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ATAC-seq problem with STAR - Multimapping reads
... Hi, I have a doubt with STAR in ATAC-seq analysis. When I have performed the alignment, i have obtained I big amount of multi-mapping reads. Now I need this data for ATAC-seq, and I do not know if I have to remove all the multimapping reads, an keep only the Uniquely mapped reads, or allow STAR to ...
chip-seq atac-seq star written 3 months ago by rafaelsolersanblas30
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Comment: C: Computational Biology Programming Course/Book
... ¡¡Thanks a lot!! :). ...
written 4 months ago by rafaelsolersanblas30
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Comment: C: Computational Biology Programming Course/Book
... I am a Biologist with 2 Master's degrees. One of them in Molecular Bioscience, and the other in Bioinformatics and Biostatistics. I know the basics about Python, R, bash etc, and I know how to use the programs that are already made. Now I wanted to take one more step, and learn how to create my own ...
written 4 months ago by rafaelsolersanblas30
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Computational Biology Programming Course/Book
... I am looking for a course / book to become an expert in programming focused on computational biology and omics (that is, not on learning how to use existing techniques such as DESeq2 or CellRanger for example, but learning how to create packages or programs from pure code. Do you recommend a course ...
scrna-seq course code programming written 4 months ago by rafaelsolersanblas30 • updated 4 months ago by jared.andrews078.6k
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GSEA preranked with DESeq2 in a RNA-seq
... Hi! I am trying to perform a GSEA preranked analysis from a paired RNAseq analysis, and I have 2 questions: - When the DESeq2 analysis is performed, a lot of genes include NAs values inside the dataframe, in the columns of Log2FC, padj, etc. To perform the GSEA, we have to use ALL the genes, and I ...
deseq2 rna-seq preranked gsea written 5 months ago by rafaelsolersanblas30 • updated 5 months ago by ATpoint46k
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Comment: A: I need help with Starsolo and scRNA-seq
... And which rownames should be ?? > assay(sce, "counts") 55487 x 992 sparse Matrix of class "dgCMatrix" [[ suppressing 77 column names ‘AAACCTGGTCTCGTTC’, ‘AAACGGGAGCCACGTC’, ‘AAACGGGAGCGAGAAA’ ... ]] [[ suppressing 77 column names ‘AAACCTGGTCTCGTTC’, ‘AAACGGGAGCCACGTC’, ‘AA ...
written 5 months ago by rafaelsolersanblas30

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