User: williamsbrian5064

Reputation:
100
Status:
Trusted
Location:
Last seen:
2 hours ago
Joined:
1 year, 1 month ago
Email:
w****************@gmail.com

Posts by williamsbrian5064

<prev • 102 results • page 1 of 11 • next >
12
votes
1
answer
175
views
5 follow
1
answer
How to add gene symbol to RNA-Seq data using R
... Hi, So I am trying to add the gene ID to my RNA-Seq data. So what I did was use Salmon to quantify my reads but instead of doing some DE analysis, I want to try and us an alternative program to try and do a little machine learning. So I really just need add the gene symbol next to the transcript ID ...
R rna-seq written 9 days ago by williamsbrian5064100 • updated 9 days ago by Ram17k
0
votes
1
answer
152
views
1
answers
Comment: C: How to change conditions in DESeq2
... Kevin! You're the man! Sorry for the late response, I was trying to get your second option to work. I really appreciate your response! I was able to get both of your options to work. I had to play with what you wrote a bit. I had to run the following to get the data in the right order MyData ...
written 4 weeks ago by williamsbrian5064100
4
votes
1
answer
152
views
1
answer
How to change conditions in DESeq2
... Hi, I am kind of new to R so I apologize if I don't give all the info that is need. I will keep and eye on this post and add any additional info that is requested. So I have two conditions in my dataset, fed and starved. The "fed" samples are my controls and the "starved" samples are my affected. S ...
R rna-seq written 4 weeks ago by williamsbrian5064100 • updated 4 weeks ago by Kevin Blighe28k
0
votes
1
answer
177
views
1
answers
Comment: C: DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' mu
... Amazing! Both of those worked like a charm. I apologize, I didn't realize I forgot to add a couple lines of regarding `[select,]` but you figured it out. I was able to mesh the two so the plots aren't massive. Thanks so much for taking the time to help me! I really really appreciate the help Kevin! ...
written 5 weeks ago by williamsbrian5064100
0
votes
1
answer
177
views
1
answers
Comment: C: DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' mu
... I was really thrown off by that as well. It took me awhile how to figure out how to change the rownames in dds ...
written 5 weeks ago by williamsbrian5064100
3
votes
1
answer
177
views
1
answer
DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' must not be length 0
... Hi, I am attempting to make some heat maps with some RNA-Seq data. I used Salmon for my quantification and followed [this][1] link to import my data into R so I can use Deseq2. So I am just going through the Deseq2 little tutorial [here][2]. I am trying to follow their instruction on how to create ...
software error R rna-seq written 5 weeks ago by williamsbrian5064100
0
votes
0
answers
174
views
0
answers
Comment: C: Issue with Samtools variant calling
... I am using version 1.8 ...
written 12 weeks ago by williamsbrian5064100
0
votes
0
answers
174
views
0
answers
Comment: C: Issue with Samtools variant calling
... Ahhh I tried using `samtools bam2fq` but was disappointed with the lack of options. I didn't realize `samtools fastq` had so many more options. I will give that a try. How do you check the sorting by readname of a bam file? ...
written 12 weeks ago by williamsbrian5064100
0
votes
0
answers
174
views
0
answers
Comment: C: Issue with Samtools variant calling
... These files were different from my other posts. These were not split up by chromosome. I have to revert the bam files back to fastq files because there was an updated genome that came out and I want to align it to the updated genome. ...
written 12 weeks ago by williamsbrian5064100
4
votes
0
answers
174
views
5 follow
0
answers
Issue with Samtools variant calling
... Hi, I had a similar question about this last week but wasn't super clear about what I was asking. I have some old bam files that I don't have the original fastq files for. I tried using picard Samtofastq but I am having an issues when I realign the reads. I have been using picard to revert the old ...
genome assembly alignment written 12 weeks ago by williamsbrian5064100 • updated 4 weeks ago by Biostar ♦♦ 20

Latest awards to williamsbrian5064

Centurion 5 weeks ago, created 100 posts.
Supporter 4 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1988 users visited in the last hour