User: jkkim

gravatar for jkkim
jkkim20
Reputation:
20
Status:
New User
Location:
S.Korea
Website:
https://github.com/hey...
Last seen:
3 days, 5 hours ago
Joined:
1 year, 7 months ago
Email:
j*********@gmail.com

Posts by jkkim

<prev • 7 results • page 1 of 1 • next >
1
vote
3
answers
259
views
3
answers
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 9 weeks ago by jkkim20 • updated 9 weeks ago by finswimmer6.2k
1
vote
2
answers
603
views
2
answers
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 6 months ago by jkkim20
0
votes
1
answer
930
views
1
answers
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 8 months ago by jkkim20
1
vote
1
answer
930
views
1
answer
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 8 months ago by jkkim20 • updated 8 months ago by Macspider2.6k
0
votes
1
answer
104
views
1
answers
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 12 months ago by jkkim20
0
votes
1
answer
104
views
1
answers
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 12 months ago by jkkim20
0
votes
5
answers
53k
views
5
answers
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 19 months ago by jkkim20

Latest awards to jkkim

Supporter 11 months ago, voted at least 25 times.
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 738 users visited in the last hour