User: Batu

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Batu110
Reputation:
110
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Last seen:
6 days, 9 hours ago
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11 months ago
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Posts by Batu

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Confusion of TF-gene interactions database
... That website is not suitable for me, I cannot extract TF-gene interaction list from there. But it seems like an interesting website, thanks... ...
written 24 days ago by Batu110
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Confusion of TF-gene interactions database
... I'm looking for a database that includes the list of TF-gene interactions which are found experimentally (not predicted). There are some posts about this here, but I wanted to ask again, because I had some confusion as I told below. I will use the list in DREM 2.0. It already includes a such list, ...
transcription factor interaction tf tf-gene written 6 weeks ago by Batu110 • updated 6 weeks ago by biostart280
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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 3 months ago by Batu110 • updated 3 months ago by EagleEye6.2k
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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 4 months ago by Batu110
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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 4 months ago by Batu110 • updated 4 months ago by Friederike2.5k
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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 4 months ago by Batu110 • updated 4 months ago by Devon Ryan88k
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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 4 months 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 4 months 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 4 months 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 4 months ago by Batu110

Latest awards to Batu

Supporter 4 months ago, voted at least 25 times.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 5 months ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 6 months ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Scholar 6 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?

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