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349 results • Page
3 of 7
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Votes
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0
votes
0
replies
8
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
27 minutes ago by
Mohamed Abderrahmane
▴ 10
0
votes
1
reply
146
views
Snakemake wrapper issue
fastqc
snakemake
updated 16 days ago by
Ram
43k • written 16 days ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
171
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization
scRNA
Seurat
7 days ago by
sakura
• 0
0
votes
0
replies
115
views
Visium dataset distance between spots calculations
SpatialSeq
Visium
updated 2 days ago by
GenoMax
140k • written 2 days ago by
houssi301
• 0
0
votes
0
replies
151
views
Correct genome version for ncbi37
ensembl
biomart
26 days ago by
ramiro.barrantes
• 0
0
votes
2
replies
196
views
Weird Basecalled reads PHRED quality plot from pycoQC
pycoQC
nanopore
sequencing
14 days ago by
njornet
▴ 10
0
votes
3
replies
333
views
Tools and software to visualize the moving cell compartments in 3D
3D-visualization
cell-compartments
20 days ago by
saamar.rajput
▴ 70
0
votes
10
replies
778
views
Problem running scPred
scPred
scPredict
updated 14 days ago by
Ram
43k • written 12 weeks ago by
Nitin
• 0
0
votes
0
replies
346
views
what is the insertPenalty for -U option of bwa mem?
bwa-mem
updated 29 days ago by
Ram
43k • written 19 months ago by
yifangt86
▴ 60
0
votes
1
reply
159
views
Mutation, MAF, CPTAC-3
CPTAC
mutation
updated 22 days ago by
marco.barr
▴ 30 • written 22 days ago by
Rob
▴ 170
0
votes
0
replies
91
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
0
replies
118
views
MG-RAST KEGG KO Search
mg-rast
kegg
metagenomics
ko
16 days ago by
Jeremy
▴ 880
0
votes
1
reply
185
views
PEAR seems to have sense to me
PEAR
updated 7 days ago by
GenoMax
140k • written 8 days ago by
ManuelDB
▴ 80
0
votes
7
replies
389
views
Error "ckalloc: request for negative space" about multiz
multiz
23 days ago by
marh32
• 0
0
votes
1
reply
199
views
Pathway activity in Bulk-RNA-SEQ analysis
R
RNA-seq
transcriptomics
updated 13 days ago by
jared.andrews07
★ 16k • written 13 days ago by
PBC
▴ 10
0
votes
7
replies
439
views
Using VEP annotation output as the input for a second VEP annotation
VCF
VEP
Annotation
updated 15 days ago by
Ram
43k • written 8 weeks ago by
Arton
• 0
0
votes
0
replies
163
views
working with shapeit.
shapeit
6 days ago by
sanchit000singhdr098
• 0
0
votes
0
replies
102
views
Calculate PSI values for pre-called splicing events in GFF from new fastq files
alternative
spladder
PSI
splicing
22 days ago by
sckinta
▴ 730
0
votes
3
replies
270
views
bioinformatics
bioinformatics
updated 21 days ago by
GenoMax
140k • written 21 days ago by
reachedahead225
• 0
0
votes
0
replies
91
views
How to access an image (slice) of interest in spatial analysis
spatial-transcriptomics
Seurat
Visium
updated 2 days ago by
Ram
43k • written 2 days ago by
piotto
▴ 20
0
votes
1
reply
125
views
Bed file
bedfile
updated 14 days ago by
Pierre Lindenbaum
160k • written 14 days ago by
Jeet
• 0
0
votes
0
replies
234
views
help a general guideline of bioinformatics strategy to analize gut metagenome virome data from stool samples
in
Guideline
virome
gut
updated 26 days ago by
Pierre Lindenbaum
160k • written 26 days ago by
Israel
• 0
0
votes
1
reply
236
views
updateR() error
R
update
updated 10 days ago by
dthorbur
★ 1.7k • written 13 days ago by
marco.barr
▴ 30
0
votes
1
reply
221
views
deepTools computeMatrix output import into R for enrichment calculations
R
deeptools
computeMatrix
deepTools
updated 12 days ago by
Pierre Lindenbaum
160k • written 12 days ago by
eeb74
• 0
0
votes
0
replies
99
views
MIRA runs yielding different assemblies with same input data and parameters
MIRA
replication
denovo
assembly
16 days ago by
btc347
• 0
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
0
votes
1
reply
146
views
Karytotype color annotations
karyotype
annotations
chromosome
color
updated 2 days ago by
Pierre Lindenbaum
160k • written 2 days ago by
Mary
• 0
0
votes
0
replies
61
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
13 hours ago by
Chris
▴ 260
0
votes
2
replies
195
views
FASTA/FASTQ files of fetal Aneuploids
nipt
10 days ago by
lolbye_1
• 0
0
votes
0
replies
107
views
Issue to run gatk4 spark
gatk
spark
15 days ago by
Mojtaba
• 0
0
votes
7
replies
310
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 17 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
0
replies
104
views
Signac LinkPeaks warning about feature.weights
R
signac
linkpeaks
17 days ago by
asap_student
• 0
0
votes
3
replies
297
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
6 days ago by
kabir.deb
▴ 80
0
votes
0
replies
141
views
Analyzing differentially methylated regions from Nanopore long read data?
bioinformatics
Long
read
sequencing
methylation
11 days ago by
Arton
• 0
0
votes
0
replies
372
views
Guidance Needed: Matching Cancer-Specific Alterations with ATAC-seq Genomic Coordinates
Alignment
ATAC-seq
Cancer
16 days ago by
davoudamirimehr
• 0
0
votes
0
replies
112
views
SAMstat mapping quality report MAPQ gt vs MAPQ lt
Sequencing
mapping
samstat
16 days ago by
njornet
▴ 10
0
votes
0
replies
105
views
t2t Reference gtf file
t2t
2 days ago by
Emre
• 0
0
votes
0
replies
129
views
samsift can't find the AS tag to filter a bam file generated using bowtie2
samsift
bowtie2
updated 28 days ago by
Ram
43k • written 28 days ago by
michael.flower.14
▴ 180
0
votes
0
replies
1.1k
views
Effect of dbSNP build differences in variant calling
GRCh38
dbSNP
variant-calling
GATK
assembly
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
0
votes
0
replies
336
views
Benchmarking pipeline for Variant identification using RNA-seq data
RNA-seq
somatic
Variant-calling
germline
updated 2 days ago by
Ram
43k • written 17 months ago by
ahkam.s
• 0
0
votes
0
replies
97
views
Best codeml model for estimating omega, M0 ?
codeml
ete3
evol
2 days ago by
Adrian Pelin
★ 2.6k
0
votes
0
replies
115
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
9 days ago by
mhale
• 0
0
votes
0
replies
85
views
How can validate hub genes or significant factors using area under the ROC curve (AUC)?
R
AUC
genes
hub
validation
14 days ago by
wyt1995
▴ 30
0
votes
0
replies
125
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 9 days ago by
Ram
43k • written 9 days ago by
shasabhi1
• 0
0
votes
0
replies
137
views
Predictor of Activation Domains
Protein
Domain
29 days ago by
buhbs
▴ 30
0
votes
1
reply
198
views
Extract Umi sequence to readname
Sequence
FgBio
UMI
updated 7 days ago by
GenoMax
140k • written 7 days ago by
Smilesky
• 0
0
votes
2
replies
270
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 2 days ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
0
votes
2
replies
287
views
PopGenome lost individual information
PopGenome
1 day ago by
Yixuan
• 0
0
votes
4
replies
330
views
PCA Plot in Single-cell RNA-seq Data
RNA-seq
PCA
single
cell
29 days ago by
Darya
• 0
0
votes
0
replies
134
views
How can we deal with converted probe id in microarray?
R
microarray
probe
ensembl
updated 21 days ago by
Ram
43k • written 22 days ago by
wyt1995
▴ 30
349 results • Page
3 of 7
Recent Votes
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Comment: Gene reads all zero for each sample
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Comment: Volcano Plot Output Inquiry: Graphs Facing Down
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Perhaps more concerning is why you have features (genes?) with small pvalue but fold-change very close to zero. It's also unusual that ther…
Comment: Gene reads all zero for each sample
by
DYLAN NICO
• 0
Thank you for the suggestions. Unfortunately I cannot add any details for lack of information. But I will try using a different alignment a…
Comment: struggle to get fasta files from ucsc goldenPath
by
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★ 1.2k
They are +ve and -ve strands, but identical two by two ... I can filter that out later on. This is probably a very naive question, but what…
Comment: Gene reads all zero for each sample
by
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81k
Do I understand correctly that you have one gene you are interested in, but all counts are zero, right? If so, first thing could be to use …
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You should use `cat` on .gz files, part of the magic of .gz ...I guess if you use `zcat` they are unzipped and this is why you get the erro…
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thank you !!
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You can only have one active token at a time, but you can copy the same token as many times as you want and use them in different computers…
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by
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▴ 120
Yes, thats correct. A lot of the responses are addressing problems other than the one I have - I don't want to cluster the sequences based …
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
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43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did run the `JoinLayers()` even then it is not working, here is the output before and after ```r DefaultAssay(combined1) <- 'RNA' com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
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140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
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Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
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thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
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