User: Batu

gravatar for Batu
Batu170
Reputation:
170
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Twitter:
cakirb_
Last seen:
3 months, 4 weeks ago
Joined:
1 year, 8 months ago
Email:
b********@gmail.com

Posts by Batu

<prev • 41 results • page 1 of 5 • next >
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Answer: A: Transcription factor targets for Human and Mouse genes
... Hi, There are some other good databases like ChIP-X or TRANSFAC databases in Harmonizome. You can find by filtering 'transcription factors' from there. : http://amp.pharm.mssm.edu/Harmonizome/download There is also a GitHub page that covers some databases for same purpose: https://github.com/slowk ...
written 5 months ago by Batu170
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Answer: A: Cannot read loom file in scanpy
... I could solve this problem thanks to @ahy1221 [in GitHub.][1] The problem is solved by removing @graphs from Seurat object. Now I have another error: --------------------------------------------------------------------------- Exception Traceback (most recent ...
written 6 months ago by Batu170
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Comment: C: Cannot read loom file in scanpy
... Yeah I've tried it before. I want to read loom to convert it into h5ad, when I open with `loompy.connect`, it fails and gives this error: AttributeError: 'LoomConnection' object has no attribute 'write' ...
written 7 months ago by Batu170
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Cannot read loom file in scanpy
... I have a loom file created from Seurat object by using `as.loom` function in Seurat3. After closing the file with `$close.all()`, I'm trying to read loom file by `read_loom` function in scanpy, but I have this error: --------------------------------------------------------------------------- ...
single-cell loom seurat written 7 months ago by Batu170
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Comment: C: Running 3 FASTQ files for WGBS
... Thank you very much... ...
written 8 months ago by Batu170
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Running 3 FASTQ files for WGBS
... I want to run some FASTQ files for WGBS, but there are 3 files for each sample [as here][1]. These are SRRxxx, SRRxxx_1 and SRRxxx_2 files. 1 and 2 are supposed to be paired-end files (~25GB each), but ENA shows the library layout as single (I've seen some other paired-end-looking samples have singl ...
fastq methylation wgbs written 8 months ago by Batu170
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Answer: A: Transcription factor binding sites using ATAC-seq peaks
... I've seen this paper and tool yesterday. Hope they can help. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1642-2 https://github.com/CostaLab/reg-gen#readme ...
written 8 months ago by Batu170
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Answer: A: Problem in indexing toplevel genome with HISAT2
... It worked after unpacking the genome. I couldn't figure out that gzipped files won't work whereas they work with main hisat2 command. Problem solved! ...
written 8 months ago by Batu170
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Comment: C: Problem in indexing toplevel genome with HISAT2
... Yes, it worked after unpacking. Gzipped files normally work with main hisat2 command, therefore I couldn't think about this reason. Thank you... ...
written 8 months ago by Batu170
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Problem in indexing toplevel genome with HISAT2
... [As I mentioned in my old post,][1] I was unable to index a toplevel genome (both unmasked and soft-masked) with HISAT2. I still have problems with that. I'm using command as below: `hisat2-build -f Mus_musculus.GRCm38.dna.toplevel.fa.gz Cm3895_ht2/GRCm38` Firstly, it gives these warnings in lots o ...
genome hisat2 hisat2-build rna-seq index written 8 months ago by Batu170

Latest awards to Batu

Scholar 5 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 8 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?
Supporter 13 months ago, voted at least 25 times.
Teacher 13 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 15 months ago, created an answer with at least 3 up-votes. For A: Anyone using Ubuntu on Windows (WSL)?
Scholar 15 months ago, created an answer that has been accepted. For A: Segmentation failed (core dumped) error in featureCounts
Scholar 15 months ago, created an answer that has been accepted. For A: Anyone using Ubuntu on Windows (WSL)?

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