User: Batu

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Batu170
Reputation:
170
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cakirb_
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4 months, 2 weeks ago
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1 year, 8 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 9 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 9 months ago by Batu170 • updated 9 months ago by caggtaagtat900
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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 10 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 11 months ago by Batu170 • updated 11 months ago by biostart310
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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 13 months ago by Batu170 • updated 13 months ago by EagleEye6.5k
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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 13 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 13 months ago by Batu170 • updated 13 months ago by Friederike5.2k
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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 14 months ago by Batu170 • updated 14 months ago by Devon Ryan93k
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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 14 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 14 months ago by Batu170

Latest awards to Batu

Scholar 6 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?
Popular Question 6 months ago, created a question with more than 1,000 views. For Anyone using Ubuntu on Windows (WSL)?
Scholar 9 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?
Supporter 14 months ago, voted at least 25 times.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 14 months ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 16 months ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Scholar 16 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?

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