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24 results • Page
1 of 1
Sort: Views
Rank
Views
Votes
Replies
0
votes
2
replies
780
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure
pymol
protein
pdb
python
41 minutes ago by
Aatif Hashmi
• 0
1
vote
1
reply
556
views
target vs. bait BED files for Illumina WES
sequencing
Illumina
WES
whole-exome
updated 2 hours ago by
Sounkou-bioinfo
• 0 • written 10 months ago by
Juan Cordero
▴ 120
4
votes
5
replies
343
views
Does adding reads cause batch effects?
kallisto
RNAseq
21 hours ago by
bioinfo
▴ 80
1
vote
2
replies
230
views
If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam file, do I have to re-sort and re-mark duplicates?
read
groups
bam
addorreplacereadgroups
12 hours ago by
javiflaja
• 0
0
votes
2
replies
229
views
How do I calculate differential expression for RNA-seq values with the "limma" package and the "ebayes" function?
differential-expression
TPM
GSEA
PANDA
16 hours ago by
John
• 0
1
vote
4
replies
207
views
Normalized counts bulk RNA-seq to DEGs
RNA-seq
updated 22 hours ago by
ATpoint
73k • written 1 day ago by
t.ru
▴ 20
0
votes
1
reply
172
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
updated 22 hours ago by
lcj34
▴ 230 • written 3 days ago by
xeod21
• 0
1
vote
1
reply
149
views
UCSC genome browser
Genome-browser
shannon-entropy
updated 21 hours ago by
Ram
39k • written 1 day ago by
Lkhagvadulam
• 0
0
votes
2
replies
144
views
Blast reads classification
NGS
magicblast
blast
updated 20 hours ago by
Ram
39k • written 1 day ago by
Giulia.cosenza
▴ 80
0
votes
1
reply
137
views
How to add annotation columns with specific colors to the heatmap?
R
heatmap
RNA-seq
updated 21 hours ago by
Ram
39k • written 1 day ago by
ahmad mousavi
▴ 750
4
votes
7
replies
132
views
conda: command not found: gatk.
conda
gatk
updated 10 minutes ago by
GenoMax
130k • written 4 hours ago by
bestone
▴ 20
1
vote
1
reply
114
views
Plotting GO enrichment DATA
R
GO
enrichment-analysis
updated 21 hours ago by
Ram
39k • written 1 day ago by
hellokwmin
• 0
0
votes
1
reply
106
views
GSEA application not launching
GSEA
updated 17 hours ago by
GenoMax
130k • written 17 hours ago by
Jen
▴ 40
0
votes
0
replies
102
views
Copy Number Alteration and Loss or Heterozygosity
LOH
CNA
copy-number
updated 21 hours ago by
Ram
39k • written 1 day ago by
Bogdan
★ 1.3k
0
votes
0
replies
88
views
How to create a haplotype map?
picard
haplotype
CrosscheckFingerprints
updated 20 hours ago by
Ram
39k • written 1 day ago by
jgarces
▴ 30
0
votes
0
replies
84
views
How are the reads assigned to genes in strand-specific RNAseq libraries?
strand-specific
strandness
RNAseq
16 hours ago by
Sib
▴ 40
0
votes
0
replies
74
views
Changing gap open and extension penalties in muscle (or any other command line tool that works on mac, really)
multiple
sequence
alignment
15 hours ago by
sodiumnitrate
▴ 20
0
votes
0
replies
72
views
question related to novel mirna file from miRDeep2?
miRDeep2
21 hours ago by
kuttibiotech2009
▴ 30
0
votes
0
replies
71
views
Using Tumor Immune Dysfunction and Exclusion (TIDE)
TPM
cancer
r
updated 20 hours ago by
Ram
39k • written 21 hours ago by
JACKY
▴ 100
1
vote
1
reply
56
views
A question about the raw RNA-seq processing workflow
GDC
RNA-seq
STAR
Ubuntu
updated 3 hours ago by
Dr William Klubinski
▴ 100 • written 3 hours ago by
wyt1995
▴ 10
1
vote
1
reply
52
views
Filtering content in heatmap to highest values
R
heamap
ggplot
updated 2 hours ago by
Papyrus
★ 2.5k • written 3 hours ago by
cthangav
▴ 50
0
votes
0
replies
22
views
I don't really understand what fold mean means
fold
1 hour ago by
ManuelDB
▴ 40
0
votes
0
replies
11
views
cannot find genes with abricate and VFDB
abricate
wgs
vfdb
1 hour ago by
luciano.g
• 0
0
votes
0
replies
3
views
how to ensure that embedding for the new data is initialized based on the embedding of the existing data in UMAP?
UMAP
10 minutes ago by
Raheleh
▴ 250
24 results • Page
1 of 1
Recent Votes
Tools To Calculate Average Coverage For A Bam File?
Comment: conda: command not found: gatk.
Answer: Finding Enhancers using Genomation library
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
Answer: Extract variants/SNPs with T>G substitution from a VCF file
Comment: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
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Recent Replies
Comment: conda: command not found: gatk.
by
GenoMax
130k
Follow directions provided by `GATK` project: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-…
Answer: What's the correct way to store bam record in a vector and free them?
by
Pierre Lindenbaum
155k
You should allocate a new pointer for each SAM record. I would do something like this (not tested): ``` std::vector<bam1_t*> record_list…
Comment: Creating a local version of Clustered NR database
by
GenoMax
130k
Thanks for those stats. So using clustered `nr` will still require significant hardware. Though this will save time as well.
Comment: Can I send my PyMol results to a web-page as a result for a submitted query? If
by
Aatif Hashmi
• 0
Basically I only want to show bases with disulphide bonds. like imagine I have a disulphide bond at 68 cys residue along with 145 cys. I …
Answer: How do I specify the Recalibration_data.table for "PrintReads" in GATK 4.3, if t
by
Pierre Lindenbaum
155k
do you want ApplyBQSR "Apply base quality score recalibration " ? https://gatk.broadinstitute.org/hc/en-us/articles/360036856671-ApplyBQSR
Comment: target vs. bait BED files for Illumina WES
by
Sounkou-bioinfo
• 0
Hi @jacorvar , did you find the answer to that question ?
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴ 100
That's an excellent point. A significant number of students are engaged in academic misconduct due to the use of fabricated references and …
Comment: Filtering content in heatmap to highest values
by
Papyrus
★ 2.5k
You mean something like this? depends on how you define "top" row or column # Create example (it is a data.table) ListerTFHeat <- …
Comment: conda: command not found: gatk.
by
666billgaytes
▴ 10
Could there be an issue with your OS? I find a lot of colleagues having problems with Mac OS and much less if none at all on Windows.
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴ 100
Great initiative :D
Answer: Extract variants/SNPs with T>G substitution from a VCF file
by
4galaxy77
2.7k
Use ```bcftools view``` with the `-i` flag for including variants. ``` bcftools view -i'REF=="T" & AlT == "G"' ```
Comment: A question about the raw RNA-seq processing workflow
by
Dr William Klubinski
▴ 100
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity
by
Ben_Ensembl
★ 2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post: https://www.ensembl.inf…
Comment: conda: command not found: gatk.
by
bestone
▴ 20
Is there anyone who can help me with this?
Comment: conda: command not found: gatk.
by
bestone
▴ 20
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
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