User: camerond
camerond • 150
- Reputation:
- 150
- Status:
- Trusted
- Location:
- Cardiff
- Last seen:
- 1 week, 2 days ago
- Joined:
- 2 years, 8 months ago
- Email:
- c*******@cardiff.ac.uk
Posts by camerond
<prev
• 40 results •
page 1 of 4 •
next >
0
votes
1
answer
135
views
1
answers
... Yes - that's the one. Many Thanks. Wrong function! ...
written 4 weeks ago by
camerond • 150
2
votes
1
answer
135
views
1
answer
... I'm trying to create a cluster plot in Seurat where instead of the cluster colours being determined by cluster IDs, they are determined by the the transcripts per cell (`nCount_RNA`).
I have tried to use the `DimPlot()` function for this:
DimPlot(rna, reduction = "umap", label = TRUE, group.by ...
written 4 weeks ago by
camerond • 150
• updated
4 weeks ago by
rpolicastro • 2.3k
0
votes
0
answers
360
views
0
answers
... I understand that. The issue is that the `/path/to/file/` and `filenames` of the original 120 files have no consistency. This was the main reason for using pandas in the first rule, in order to standardise, or to use your term, normalise the sample/filenames so that I could start using the typical ` ...
written 4 months ago by
camerond • 150
0
votes
0
answers
360
views
0
answers
... Ah ... I didn't know that. Thanks for the heads up! ...
written 4 months ago by
camerond • 150
0
votes
0
answers
360
views
0
answers
... No probs. Fair points. Most of the snakemake walkthrough/tutorials describe the functionality of `{wildcards}` in relation to a single `{wildcard}` that remains constant and flows through the most, if not all of the rules i.e. `{sample}`. I've yet to find one that describes the best way do deal with ...
written 4 months ago by
camerond • 150
0
votes
0
answers
360
views
0
answers
... Response to first post: Probably, yes. However, I was hoping to standardise the `{wildcards}` across the rules. Your suggestion would add more `{wildcards}`, but that may be the cleanest way to do it. What do you mean pandas may be overkill? What would you suggest as an alternative? ...
written 4 months ago by
camerond • 150
0
votes
0
answers
360
views
0
answers
... Thanks for your suggestions. Re: if statement - Although I think both work, your way is less verbose so I have changed it in the IP.
...
written 4 months ago by
camerond • 150
4
votes
0
answers
360
views
0
answers
... In my current project, I have ~560 RNA-seq fastq files (120 samples) that were sequenced in various locations. As such, the naming structure of the files are different, some files are zipped and some are unzipped, the files are dotted around our databank in various locations and the sample ID for ea ...
written 4 months ago by
camerond • 150
0
votes
1
answer
290
views
1
answers
... No probs. Many Thanks. ...
written 9 months ago by
camerond • 150
0
votes
1
answer
290
views
1
answers
... I'm hoping only half the reads will have Ns in them. I'll def filter these out first. Many thanks for the suggestion. ...
written 9 months ago by
camerond • 150
Latest awards to camerond
Popular Question
22 days ago,
created a question with more than 1,000 views.
For Obtaining rsIDs using BiomaRt or linux
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Get rsID for a list of SNPs in an entire GWAS sumstats file
Great Question
8 months ago,
created a question with more than 5,000 views.
For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Appreciated
12 months ago,
created a post with more than 5 votes.
For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Student
14 months ago,
asked a question with at least 3 up-votes.
For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Supporter
18 months ago,
voted at least 25 times.
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Get rsID for a list of SNPs in an entire GWAS sumstats file
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2194 users visited in the last hour