User: Batu

gravatar for Batu
Batu100
Reputation:
100
Status:
Trusted
Location:
Twitter:
cakirb_
Last seen:
15 hours ago
Joined:
7 months ago
Email:
b********@gmail.com

Posts by Batu

<prev • 26 results • page 1 of 3 • next >
0
votes
0
answers
42
views
0
answers
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 16 hours ago by Batu100
10
votes
2
answers
120
views
6 follow
2
answers
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 3 days ago by Batu100 • updated 3 days ago by Friederike2.3k
5
votes
1
answer
126
views
1
answer
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 17 days ago by Batu100 • updated 17 days ago by Devon Ryan85k
0
votes
0
answers
199
views
0
answers
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 18 days ago by Batu100
0
votes
0
answers
199
views
0
answers
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 It is really easy to use them, but isn't it outdated?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 18 days ago by Batu100
3
votes
0
answers
400
views
0
answers
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 18 days ago by Batu100
6
votes
0
answers
199
views
6 follow
0
answers
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 21 days ago by Batu100
1
vote
1
answer
98
views
1
answers
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 4 weeks ago by Batu100
1
vote
1
answer
98
views
1
answer
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 4 weeks ago by Batu100
4
votes
1
answer
427
views
1
answers
Answer: A: Anyone using Ubuntu on Windows (WSL)?
... Workaround for this problem is to recompile subread package with the recent glibc (https://github.com/Microsoft/WSL/issues/3391). To do that, update glibc to the newest version (2.23), and then compile the source of the package, and introduce its "bin" directory to path. Problem solved!! ...
written 10 weeks ago by Batu100

Latest awards to Batu

Supporter 11 days ago, voted at least 25 times.
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 4 weeks ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Scholar 10 weeks ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 624 users visited in the last hour