User: from the mountains
from the mountains • 130
- Reputation:
- 130
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 1 day, 18 hours ago
- Joined:
- 6 years ago
- Email:
- a************@gmail.com
Posts by from the mountains
<prev
• 68 results •
page 1 of 7 •
next >
2
votes
1
answer
85
views
1
answers
... Do you mean cell type, rather than cell name? Seurat doesn't automatically annotate your cells with the cell type. You can do that through manual intervention with the `RenameIdents` function, or you can get the `SingleR` package from bioconductor to "guess" it for you. you can get the current ident ...
written 10 days ago by
from the mountains • 130
0
votes
0
answers
503
views
0
answers
Comment:
C: Qualimap out of memory
... I don't usually use qualimap on rna data but 1.2 Gb is usually insufficient for my exome bams, regardless of the amount of available memory. ...
written 6 weeks ago by
from the mountains • 130
0
votes
0
answers
681
views
0
answers
... doesn't this do exactly that in vcftools?
https://github.com/vcftools/vcftools/blob/master/src/perl/vcf-convert ...
written 7 weeks ago by
from the mountains • 130
0
votes
0
answers
233
views
0
answers
... I am using GATK 4.1.0.0 to mark duplicates in and recalibrate my bam. My workflow is currently to use:
1. MarkDuplicates
2. BaseRecalibrator
3. ApplyBQSR
But recently I have wanted to replace them with spark enabled pipelines to increase efficiency. I came across ReadsPipelineSpark, which marks dup ...
written 12 weeks ago by
from the mountains • 130
0
votes
0
answers
335
views
0
answers
... wouldn't you want to know if RNase treatment even worked, even if your provider says they performed it? ...
written 6 months ago by
from the mountains • 130
0
votes
0
answers
335
views
0
answers
... not sure how my previous reply didn't show up so maybe i'm double-posting. I would think you would see a lot of breakpoints coinciding with known splice sites, and maybe there's a statistical test to see if there's a preference for breakpoints at splice sites. any splice event in DNA data could be r ...
written 6 months ago by
from the mountains • 130
4
votes
0
answers
335
views
0
answers
... I am looking for any bioinformatics tool that might detect RNA contamination in DNA data (specifically exome data). Although RNA contamination is rare it's something we'd like to study on our samples nonetheless.
Edit: some ideas:
- check for rRNA contamination, something like Picard's `Collect ...
written 6 months ago by
from the mountains • 130
0
votes
1
answer
214
views
1
answers
... i've edited my comment for clarity. ...
written 7 months ago by
from the mountains • 130
0
votes
0
answers
261
views
0
answers
... I am attempting to use the `qualimap bamqc` tool to get qc information and having a bit of trouble using it for testing of small inputs. I am running the following
qualimap bamqc -bam smalldata.bam -c -gd HUMAN -gff newbed.bed -outdir outfolder
Both the bam and the bed file are "small". i thi ...
written 7 months ago by
from the mountains • 130
• updated
7 months ago by
Ram ♦ 32k
1
vote
1
answer
214
views
1
answers
... i'd add to that and say
```
grep "^#SampleID\|^ID\|s__" > extracted_file.txt
```
to make sure all matches are at the beginning of the line. you can also use option `-P` so you don't have to escape the `|` operator ...
written 7 months ago by
from the mountains • 130
Latest awards to from the mountains
Popular Question
7 months ago,
created a question with more than 1,000 views.
For bowtie issues: unable to map significant amount of pairs
Popular Question
7 months ago,
created a question with more than 1,000 views.
For bowtie issues: unable to map significant amount of pairs
Supporter
8 months ago,
voted at least 25 times.
Great Question
11 months ago,
created a question with more than 5,000 views.
For How is Tophat installed?
Popular Question
12 months ago,
created a question with more than 1,000 views.
For bowtie issues: unable to map significant amount of pairs
Popular Question
12 months ago,
created a question with more than 1,000 views.
For How is Tophat installed?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For bowtie issues: unable to map significant amount of pairs
Popular Question
21 months ago,
created a question with more than 1,000 views.
For bowtie issues: unable to map significant amount of pairs
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For bowtie issues: unable to map significant amount of pairs
Epic Question
2.3 years ago,
created a question with more than 10,000 views.
For How do I run Tophat?
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For How is Tophat installed?
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For How to run an identity-by-descent calculation on plink with a p-value threshold?
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For How is Tophat installed?
Popular Question
3.6 years ago,
created a question with more than 1,000 views.
For How is Tophat installed?
Great Question
4.0 years ago,
created a question with more than 5,000 views.
For How do I run Tophat?
Popular Question
5.8 years ago,
created a question with more than 1,000 views.
For How is Tophat installed?
Popular Question
5.8 years ago,
created a question with more than 1,000 views.
For How do I run Tophat?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2368 users visited in the last hour