User: Batu

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Batu170
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2 years, 6 months ago
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Posts by Batu

<prev • 41 results • page 2 of 5 • next >
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Comment: C: Suggestions for Trimmomatic and "illuminaclip" parameter
... Thanks, I will start to use `ILLUMINACLIP`. What about the `TRAILING` and `MINLEN` parameters? Is it suitable to use `ILLUMINACLIP`, `TRAILING` and `MINLEN` parameters for the high quality fastq's only? Due to having high quality scores, we have thought these parameters can be used like that. (`TRAI ...
written 19 months ago by Batu170
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Suggestions for Trimmomatic and "illuminaclip" parameter
... I've been using Trimmomatic by using LEADING, TRAILING and SLIDING WINDOW parameters. Recently we have seen that ILLUMINACLIP parameter is also being used mostly. Until we have seen this, we have been thinking that Trimmomatic is built to trim Illumina adapters specifically, therefore it would detec ...
trimmomatic trimming illuminaclip rna-seq written 19 months ago by Batu170 • updated 19 months ago by caggtaagtat1.3k
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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 20 months ago by Batu170
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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 20 months ago by Batu170 • updated 20 months ago by biostart350
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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 23 months ago by Batu170 • updated 23 months ago by EagleEye6.7k
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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 23 months ago by Batu170
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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 23 months ago by Batu170 • updated 23 months ago by Friederike6.1k
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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 24 months ago by Batu170 • updated 24 months ago by Devon Ryan96k
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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 24 months ago by Batu170
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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 24 months ago by Batu170

Latest awards to Batu

Popular Question 4 months ago, created a question with more than 1,000 views. For Cannot read loom file in scanpy
Popular Question 9 months ago, created a question with more than 1,000 views. For Cannot read loom file in scanpy
Popular Question 9 months ago, created a question with more than 1,000 views. For Anyone using Ubuntu on Windows (WSL)?
Popular Question 14 months ago, created a question with more than 1,000 views. For Segmentation failed (core dumped) error in featureCounts
Popular Question 14 months ago, created a question with more than 1,000 views. For Anyone using Ubuntu on Windows (WSL)?
Scholar 15 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?
Popular Question 16 months ago, created a question with more than 1,000 views. For Anyone using Ubuntu on Windows (WSL)?
Scholar 19 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?
Supporter 23 months ago, voted at least 25 times.
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Scholar 2.1 years ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?

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