gc5
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2 answers
8 votes
7k views
Are mitochondrial genes to exclude in scRNA-seq such as ribosomal genes?
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6 votes

According to Ilicic et al. (2016), on upregulation of mtRNA in broken cells: There is an extensive literature on the relationship between mtDNA, mitochondrially localized proteins, and cell death [...

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3 answers
6 votes
317 views
Fast filtering of intervals not falling within a certain distance from known genes
3 votes

First I prepared a bed file in which the gene intervals are augmented by 1KB before and after the gene start and end coordinates. Then I intersected this bed file with my original one with the option -...

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2 answers
2 votes
69 views
Why models of stochastic gene expression predict that intrinsic noise should increase as the amount of transcript decrease
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2 votes

Reading Kaufmann and van Oudenaarden (2007), it seems to validate the first alternative (using results from the Central Limit Theorem): Although biochemical fluctuations influence all stages of ...

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1 answers
1 votes
187 views
TagReadWithGene missing when using latest version of Drop-seq_tools
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1 votes

As per this response from Drop-seq_tools team, at the moment intronic regions cannot be annotated and TagReadWithGeneExon should be used instead. However, in the version of the public repository: ...

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1 answers
5 votes
388 views
Which tools for differential expression analysis in scRNA-Seq?
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1 votes

According to Jaakkola et al. (ref. 1): Based on our comparisons, DESeq and Limma without any modifications are not suitable for scRNA-seq data analysis, and yet, they have performed well in the ...

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1 answers
5 votes
499 views
Single-cell RNA sequencing (scRNA-seq): filtering cells by transcript counts, how to choose cutoffs?
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1 votes

By reading this tutorial: Wells with few reads/molecules are likely to have been broken or failed to capture a cell, and should thus be removed. This answers the first part of the question. For ...

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1 answers
0 votes
112 views
Low percentage of reads with consistent barcodes in Split-Seq run
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In my case the problem was due a wrong set of allowed round1 barcodes, therefore the filtering pipeline was removing most part of the reads. In particular, with the right barcode1 whitelist the total ...

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1 answers
0 votes
206 views
Demultiplexing and preprocessing for custom single-nucleus Drop-seq data
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I didn't notice the sentence: Paired-end sequencing reads were processed largely as described (http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf ), with ...

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