User: rafaelsolersanblas
rafaelsolersanblas • 20
- Reputation:
- 20
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- 3 days, 3 hours ago
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- 8 months, 3 weeks ago
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Posts by rafaelsolersanblas
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6
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6 follow
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... 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, ...
written 17 days ago by
rafaelsolersanblas • 20
• updated
17 days ago by
jperezboza • 20
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76
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... 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 ...
written 18 days ago by
rafaelsolersanblas • 20
0
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1
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111
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1
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... Thank you!! I will test with Bowtie2
...
written 18 days ago by
rafaelsolersanblas • 20
2
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1
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111
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1
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... 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 ...
written 18 days ago by
rafaelsolersanblas • 20
0
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1
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137
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1
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... ¡¡Thanks a lot!! :). ...
written 5 weeks ago by
rafaelsolersanblas • 20
0
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1
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137
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1
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... 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 5 weeks ago by
rafaelsolersanblas • 20
2
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1
answer
137
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1
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... 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 ...
written 5 weeks ago by
rafaelsolersanblas • 20
• updated
5 weeks ago by
jared.andrews07 ♦ 7.9k
2
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1
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133
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1
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... 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 ...
written 7 weeks ago by
rafaelsolersanblas • 20
• updated
7 weeks ago by
ATpoint ♦ 41k
0
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2
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175
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... 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 9 weeks ago by
rafaelsolersanblas • 20
0
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2
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175
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2
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... I have used the filtered, and now I have the correct number of cells! Thanks :) But I still have a number of counts in the assay to small.
> sce
class: SingleCellExperiment
dim: 55487 992
metadata(1): Samples
assays(1): counts
rownames(55487): ENSMUSG00000102693 ENSMUSG ...
written 9 weeks ago by
rafaelsolersanblas • 20
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