User: Batu

gravatar for Batu
Batu110
Reputation:
110
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cakirb_
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3 days, 21 hours ago
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8 months, 3 weeks ago
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Posts by Batu

<prev • 27 results • page 1 of 3 • next >
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No replicates in 1 group, which idea is the best to apply?
... I will analyze the dataset with 5 samples (2 samples in group1, 2 samples in group2 and 1 sample in group3). Due to having no replicates in group3, I'm confused that if I should use a certain dispersion value in edgeR which is described in its manual, or I should use DESeq2 normally without any chan ...
no replicates deseq2 rna-seq edger written 7 weeks ago by Batu110 • updated 7 weeks ago by EagleEye6.0k
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Is there any website that shows the cell type for a given marker list?
... I am looking for a website that shows possible cell types according to given marker list. [In this biostars post,][1] a marker database is recommended, but it is not able to do what I want. Any suggestions? Thanks... [1]: https://www.biostars.org/p/44984/ ...
cell biomarker clustering written 7 weeks ago by Batu110
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6 follow
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How is it possible to have more than 25000 genes in counts file?
... Hello everyone, I have a question about RNA-seq for Homo sapiens. Humans have about 25000 genes which are protein-coding. But in my recent analysis, there are more than 58000 genes with their Ensembl Gene IDs inside my counts file. How is it possible? Did I miss something while processing the fastq ...
rna-seq sequencing written 7 weeks ago by Batu110 • updated 7 weeks ago by Friederike2.3k
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Choosing human reference genome and indexing
... I have a difficulty to choose the suitable source for me. There are 3 ways that I consider to use the reference genome. I'm really confused. 1. **From HISAT2 website.** "tran" version (contains GTF) as @Carlo Yague mentioned in [my previous post][1]. [It is not updated, last version from March 201 ...
indexing reference genome rna-seq written 9 weeks ago by Batu110 • updated 9 weeks ago by Devon Ryan86k
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Comment: C: Compatibility between my reference genome and GTF file
... Now, there are 3 ways that I consider to use the reference genome. I'm really confused right now. 1. **From HISAT2 website.** "tran" version (contains GTF) as @Carlo Yague mentioned. [It is not updated, last version from March 2016, I prefer to use the updated one.] 2. **From GENCODE website.** a ...
written 10 weeks ago by Batu110
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Comment: C: Compatibility between my reference genome and GTF file
... It is really easy to use them, but isn't it outdated? (It was released more than 2 years ago according to its date on ftp) ...
written 10 weeks ago by Batu110
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Answer: A: Awk in Bioinformatics
... I can refer this link that includes more examples and other cases: [Useful bash one-liners for bioinformatics][1]. [1]: https://github.com/stephenturner/oneliners ...
written 10 weeks ago by Batu110
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Compatibility between my reference genome and GTF file
... Hello, I'm new to bioinformatics, I have a question which may seem easy. For my RNA-seq analyses, I was using HISAT2 with already-indexed reference genome downloaded from HISAT2 website for Homo sapiens. And as GTF I was using the one I downloaded from Ensembl. After some runs, I thought this usage ...
alignment reference genome rna-seq hisat2 written 10 weeks ago by Batu110
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Answer: A: Is there any way to infer percentage from the branches in trajectories plotted i
... I played with the elements inside CellDataSet object (Let's say it is 'a'). All of its data is stored in 'data' list inside this object, it can be reached with `a@data`. Inside data, you can find nGene, nUMI, cluster number... etc. for each cell. After ordering the cells with `orderCells()` function ...
written 11 weeks ago by Batu110
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Is there any way to infer percentage from the branches in trajectories plotted in Monocle?
... I would like to say that this percent of the cells choose the first branch and this percent of the cells choose second branch. Is there any way to infer this kind of percentage from trajectories plotted in Monocle? ...
single-cell R monocle single cell trajectory written 12 weeks ago by Batu110

Latest awards to Batu

Supporter 9 weeks ago, voted at least 25 times.
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 4 months ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Scholar 4 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?

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