User: Ark

gravatar for Ark
Ark40
Reputation:
40
Status:
New User
Location:
US
Last seen:
2 days, 11 hours ago
Joined:
2 months, 2 weeks ago
Email:
t*****************@gmail.com

Undergraduate bioinformatics student.

Posts by Ark

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Finding Only Protein Coding Genes from Gencode GTF
... I see, that is definitely a better approach than I am currently using. Thanks for the suggestions and the links! ...
written 2 days ago by Ark40
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Comment: C: How to "Randomly" Select Genes
... This is nice also. Looks a bit cleaner. Thanks! ...
written 7 days ago by Ark40
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Comment: C: Finding Only Protein Coding Genes from Gencode GTF
... Thanks for your response Igor! I had not seen that page. Thank you for the link! I will dig through and try to determine which labels are useful for me. Do you have any recommendations on a better way to separate the protein coding genes? I am working in R and currently I am using awk and some reg ...
written 7 days ago by Ark40
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Finding Only Protein Coding Genes from Gencode GTF
... Hello! I am trying to filter out only the protein coding genes from the gencode gtf file found here: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.basic.annotation.gtf.gz I have found a discrepancy in the way some of the genes are labeled and it has been causing me ...
R rna-seq written 7 days ago by Ark40 • updated 7 days ago by igor6.8k
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Comment: C: How to "Randomly" Select Genes
... I see, that's interesting. Earlier in my project I created an "elbow-graph" from the WSS values to attempt to gain some insight on the number of clusters I should use. It was not as helpful as I was hoping for, but I only tried it on my data, not with any "synthetic" data to compare it to. I haven't ...
written 22 days ago by Ark40
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Comment: C: How to "Randomly" Select Genes
... This looks promising! Everything I had written up to this point used for loops instead of apply and I knew there must be a better/more efficient way. The combination of sample(rep()) is particularly interesting! Thank you! ...
written 22 days ago by Ark40
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Answer: A: grep whole sequences containing a specific motif in a fasta file
... I believe that {4} that you are using is an extended regular expression and you would need to either use egrep or the -E flag with grep. I got it to work using this: grep -E 'S[A-Z]{4}[FS][A-Z]{3}L' jara3.fasta > jara4.fasta Hope that works! ...
written 23 days ago by Ark40
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How to "Randomly" Select Genes
... Hello again Biostars community! I am working on a project for my internship regarding the efficacy of different clustering techniques on RNA-seq data. I have used many different common clustering techniques in R and compared their results and the clusters they produce. Now, I have gotten to a point ...
gene R rna-seq clustering written 23 days ago by Ark40 • updated 21 days ago by zx87545.3k
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Comment: C: Confusion About Observations vs. Variables in my Data
... Thank you for clearing that up for me! I'm relieved, as I was worried that the (limited) work I had already done was going to need to be scrapped because I forgot to check the structure of my data. I won't make this mistake again! I will look into creating the columns that you mentioned also. Most ...
written 7 weeks ago by Ark40
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Confusion About Observations vs. Variables in my Data
... Hello, I am very new to bioinformatics (and statistics) and have a basic question that I haven't been able to fully answer on my own. I have been using R to do some basic analysis of RNA-seq data. I know that "tidy data" conventions say to organize my data by putting observations into rows and var ...
R beginner k-means rna-seq pca written 7 weeks ago by Ark40 • updated 7 weeks ago by RamRS18k

Latest awards to Ark

Scholar 23 days ago, created an answer that has been accepted. For A: grep whole sequences containing a specific motif in a fasta file
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: grep whole sequences containing a specific motif in a fasta file

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