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328 results • Page
2 of 7
Sort: replies
Rank
Views
Votes
Replies
1
vote
4
replies
546
views
cellranger error message
multiplexing
cellranger
updated 18 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
0
votes
4
replies
269
views
GO analysis: p-value range
GO
R
updated 8 days ago by
Matthias Zepper
4.6k • written 9 days ago by
sooni
▴ 20
1
vote
3
replies
315
views
Odd alignment question/finding
Alignment
updated 25 days ago by
barslmn
★ 2.2k • written 27 days ago by
poordumbsillyidiot
• 0
0
votes
3
replies
185
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 7 days ago by
Ram
44k • written 7 days ago by
pirku
• 0
0
votes
3
replies
318
views
Sam file Header problem
Sam
Header
problem
file
updated 11 days ago by
Pierre Lindenbaum
162k • written 12 days ago by
saifulislam99121
• 0
0
votes
3
replies
402
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 5 days ago by
ATpoint
82k • written 5 days ago by
shahzaibali
• 0
0
votes
3
replies
198
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
13 days ago by
Esraa
• 0
1
vote
3
replies
300
views
Failed to download data from EBI with ascp
EBI
aspera
updated 22 hours ago by
jude
• 0 • written 6 weeks ago by
biock
▴ 60
3
votes
3
replies
319
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 15 days ago by
Ram
44k • written 28 days ago by
Adyasha
• 0
0
votes
3
replies
239
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 21 days ago by
GenoMax
142k • written 21 days ago by
Assa Yeroslaviz
★ 1.9k
1
vote
3
replies
300
views
STAR aligner error
RNA-seq
STAR
slurm
updated 20 days ago by
Ram
44k • written 21 days ago by
M.
▴ 30
0
votes
3
replies
266
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 8 days ago by
marco.barr
▴ 130 • written 9 days ago by
Mohamed Samir
▴ 30
0
votes
3
replies
387
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 29 days ago by
Ram
44k • written 5 months ago by
Fadi
• 0
1
vote
3
replies
364
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 28 days ago by
GenoMax
142k • written 28 days ago by
jeffrey.maurer.informatics
• 0
0
votes
3
replies
238
views
How to access GWAVA software of data
GWAVA
updated 14 days ago by
GenoMax
142k • written 14 days ago by
nonaddldy
▴ 10
1
vote
3
replies
364
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
23 days ago by
Lada
▴ 30
0
votes
3
replies
353
views
KEGG Pathways
r
RNA-seq
updated 28 days ago by
Ram
44k • written 28 days ago by
Sudip
• 0
2
votes
3
replies
363
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 25 days ago by
dthorbur
★ 2.0k • written 25 days ago by
Vijith
▴ 30
0
votes
3
replies
350
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 28 days ago by
GenoMax
142k • written 29 days ago by
kim
• 0
2
votes
3
replies
393
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 19 days ago by
bk11
★ 2.5k • written 23 days ago by
Yoosef
▴ 60
1
vote
3
replies
214
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 6 days ago by
GenoMax
142k • written 7 days ago by
s
• 0
0
votes
3
replies
280
views
Software to separate reads from different individuals
software
development
nanopore
updated 29 days ago by
GenoMax
142k • written 29 days ago by
njornet
▴ 20
0
votes
3
replies
378
views
Snakemake wrapper issue
fastqc
snakemake
updated 15 days ago by
Wei-Chen Pan
• 0 • written 11 weeks ago by
Matvii Mykhailichenko
• 0
3
votes
3
replies
342
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 18 days ago by
Ram
44k • written 18 days ago by
Omics data mining
▴ 260
1
vote
2
replies
165
views
Polygenic Risk Score calculation
snp
polygene
prs
variants
17 hours ago by
ashaneev07
▴ 20
0
votes
2
replies
293
views
How can I calculate the OS of each patient?
overall-survival
8 days ago by
Pedro
• 0
1
vote
2
replies
276
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 28 days ago by
Ram
44k • written 28 days ago by
Ravita
• 0
1
vote
2
replies
288
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
4 days ago by
F110152169
• 0
1
vote
2
replies
347
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
27 days ago by
Nafi
• 0
1
vote
2
replies
227
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
21 days ago by
robert.flynn.21
• 0
0
votes
2
replies
313
views
Traveler with Infernal mapping failed
r2dt
updated 10 days ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
3
votes
2
replies
230
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 15 days ago by
ATpoint
82k • written 15 days ago by
jennyp0706
• 0
0
votes
2
replies
263
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
26 days ago by
dtnondorf
• 0
1
vote
2
replies
314
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
27 days ago by
rianna.collins
• 0
2
votes
2
replies
2.7k
views
Pindel Segmentation Fault Error
pindel
updated 24 days ago by
Ruqaiya
• 0 • written 10.3 years ago by
Yuelin
▴ 20
2
votes
2
replies
273
views
Raw counts using stringtie
stringtie
RNA-seq
updated 25 days ago by
GenoMax
142k • written 25 days ago by
ahmad.sajad4541
• 0
0
votes
2
replies
241
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
1 day ago by
marco.barr
▴ 130
1
vote
2
replies
134
views
How do I check if a DNA sequence of a gene is supported by RNAseq data?
Genetics
RNA-seq
Phase-variation
Alignment
14 hours ago by
Jack
• 0
0
votes
2
replies
218
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
7 days ago by
Shukai
• 0
0
votes
2
replies
321
views
How are score_weights calculated in this code?
single-cell
17 days ago by
carolofharvest
▴ 40
0
votes
2
replies
471
views
How to update R on ubuntu
installation
update
R
apt-get
29 days ago by
Bosberg
▴ 50
2
votes
2
replies
126
views
dbNSFP4.7a database format to Annovar Format?
snp
annovar
NGS
dbNSFP
updated 15 hours ago by
Ram
44k • written 23 hours ago by
Clark_BioMorgan
▴ 50
2
votes
2
replies
277
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
12 days ago by
bioinfo
▴ 150
0
votes
2
replies
255
views
What do the transcript variant # mean in RefSeq?
refseq
updated 5 days ago by
Ram
44k • written 5 days ago by
curious
▴ 750
1
vote
2
replies
302
views
Downloading full alignments from Pfam
pfam
23 days ago by
bef1
• 0
0
votes
2
replies
329
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 16 days ago by
Zhenyu Zhang
★ 1.2k • written 25 days ago by
yahn
• 0
0
votes
2
replies
291
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 11 days ago by
Pierre Lindenbaum
162k • written 12 days ago by
melissachua90
▴ 70
0
votes
2
replies
145
views
coding and non-coding region of the viral genome
viral-genome
9 hours ago by
Ghada
• 0
0
votes
2
replies
290
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
21 days ago by
sainavyav22
• 0
0
votes
2
replies
192
views
CreateSeuratObject taking very long
seurat
5 days ago by
eae6d2e7
• 0
328 results • Page
2 of 7
Recent Votes
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
Answer: help in changing Y scale in R
Answer: when I use htslib to write a bam. Error of "truncated file" shows by samtools
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Comment: I cannot download VG in any way
Why does WGCNA use weighted correlation instead of Pearson correlation?
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Comment: polygenic risk score
by
ashaneev07
▴ 20
Can't we calculate the prs of a single patient data with respect to GWAS data for predicting the risk for particular diseases?
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
Gordon Smyth
★ 7.2k
It is very common for studies like this to show no significant DE. Human studies like this where comparisons are made between diseases and …
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
update. The error persists. With ValidateSamFile I get no error until i use MarkDuplicates. Then for the MarkDuplicates output I get: …
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
Aaron
▴ 10
Thanks very much.
Answer: help in changing Y scale in R
by
LauferVA
4.2k
Hello @ab33b6d7 , Below is approximately the code block you provided, with a few additional lines added. Each of the new lines has > …
Comment: 2 PhD Students in single-cell bioinformatics
by
Uzma
• 0
I want to apply for this PhD position. I did MSc Zoology and MPhil biosciences.
Comment: Rseqc infer_experiment.py: 0 usable reads sampled and unknown data type
by
mazegriff
• 0
Hi pubsurfted, I ran into the same issue using a reference transcriptome with HISAT2 from the Ensembl database. For others with similar e…
Comment: Intersection of multiple vcf files
by
Jeremy Leipzig
22k
isec is pretty awful for these set operations - especially since individual samples present alleles, not lines in a VCF file. If you can co…
Comment: help in changing Y scale in R
by
Medhat
9.7k
Maybe try to calculate min and max combined_min <- min(a_filtered$value, a_filtered_tv$value, na.rm = TRUE) combined_max <- max(a_…
Answer: help in changing Y scale in R
by
ATpoint
82k
Use `+ylim(c(lower, upper))`. Either set manually, or query both `a_filtered` and `a_filtered_tv` for the minimum and maximum values that g…
Comment: Error with pheatmap - 'from' must be a finite number
by
zx8754
11k
I am not familiar with deseq data, but if it makes sense, remove rows/columns that have only NAs. #remove rows x<- mat.z[ rowSums(…
Answer: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
John Marshall
3.1k
There are several problems with this code: 1. You have not set `b->l_data`, which here should be set to the same value as `b->m_data`. T…
Comment: Best practices in Fungal Genome Assembly
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Should I use both Recon and Pilon for polshing ? Recon uses Long-reads and Pilon uses short-read. if both should be used, is their any pref…
Comment: Mutation counts corrected by number of samples
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garcesj
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How come? If I have a pro-tumorigenic product, for example, wouldn't this comparison be valid?
Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
by
Ngrin
• 0
Thanks @Zhenyu Zhang for your response. I have just looked at the files you mentioned. Do you have any recommended package or code snippet …
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