User: jkkim

gravatar for jkkim
jkkim30
Reputation:
30
Status:
New User
Location:
S.Korea
Website:
https://github.com/hey...
Last seen:
3 days, 1 hour ago
Joined:
2 years, 1 month ago
Email:
j*********@gmail.com

Posts by jkkim

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Retrieve all compound ID, Description from a ko ID
... I am sorry. For some reason, I removed the post. Sorry again. ...
written 4 months ago by jkkim30
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Comment: C: Retrieve all compound ID, Description from a ko ID
... Thank you. I tried that way before, but it doesn't have the chemical reaction information. ...
written 4 months ago by jkkim30
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Retrieve all compound ID, Description from a ko ID
... Hello, I am trying to get, reaction IDs, descriptions, compound IDs and their descriptions from ko IDs (e.g. K00163). I went through Biostars and KEGG rest APIs, but I can't find an answer. For example, I have a K00163. My goal is ko:K00507 has R02222 (Reaction ID, description) has C00001(compoun ...
rest api kegg written 4 months ago by jkkim30
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Answer: A: featureCounts and bash
... There's some tools for building pipelines. snakemake, gnu-parallel...etc. Here's some code for star alignment using gnu-parallel. It works well for me. STAR_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/" INPUT_DIR="00_raw_fastq" OUTPUT_DIR="01_alignment_genes_count" GTF=" ...
written 8 months ago by jkkim30 • updated 8 months ago by finswimmer11k
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Answer: A: HISAT2 for loop shell scripting
... I'd like to introduce snakemake for a task like this. https://snakemake.readthedocs.io/en/stable/ It's easy to use and well-documented. Here is a tutorial from Mr. Slowikowski's website. https://slowkow.com/notes/snakemake-tutorial/ And this is my mRNAseq pipeline made by snakemake. (I use STAR ...
written 12 months ago by jkkim30
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Comment: C: Building RNAseq pipeline STAR-RSEM-tximport-DESeq2
... Thank you for your comment. I have some old data based on GRCh37, So I go with GRCh37. Maybe next project I will go for GRCh38. ...
written 14 months ago by jkkim30
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Building RNAseq pipeline STAR-RSEM-tximport-DESeq2
... Hello, I did some googling about mRNAseq pipeline and built that pipeline. So I would like to know if my pipeline is okay. Reference genome : Human gencode GRCh37 Aligner : STAR Expression quantification : RSEM Gene count table convert? : tximport Statistical test : DESeq2 it seems lik ...
pipeline rna-seq written 14 months ago by jkkim30 • updated 14 months ago by Macspider2.8k
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Comment: C: snakemake about rule all
... I am sorry. I will keep that in mind. I will remove this post soon. Thank you for the answer! ...
written 18 months ago by jkkim30
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Comment: C: snakemake about rule all
... I am sorry. I will keep that in mind. I will remove this post soon. Thank you for how to ask a question the community! ...
written 18 months ago by jkkim30
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Comment: C: How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
... Thank you for the post. This is what I am looking for! ...
written 2.1 years ago by jkkim30

Latest awards to jkkim

Popular Question 5 months ago, created a question with more than 1,000 views. For Building RNAseq pipeline STAR-RSEM-tximport-DESeq2
Supporter 17 months ago, voted at least 25 times.
Autobiographer 2.1 years ago, has more than 80 characters in the information field of the user's profile.

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