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1,000 results • Page
3 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
128
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
3 days ago by
Mamatha Y S
• 0
0
votes
0
replies
125
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 2 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
507
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 3 days ago by
ATpoint
82k • written 4 days ago by
rheab1230
▴ 140
0
votes
2
replies
248
views
bam merging for archaic samples
samtools
bam
updated 2 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
7
votes
6
replies
439
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
2 days ago by
analyst
▴ 30
1
vote
1
reply
249
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 4 days ago by
Bioinformatician
• 0
1
vote
0
replies
534
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
4 days ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
290
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 4 days ago by
Ram
43k • written 4 days ago by
Nina
• 0
2
votes
5
replies
501
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 3 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
Giorgio
• 0
2
votes
1
reply
280
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 4 days ago by
GenoMax
141k • written 4 days ago by
rebecca.calvo
• 0
0
votes
0
replies
205
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
3 days ago by
abhishekghadge
• 0
2
votes
5
replies
670
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by
Jesse
▴ 740 • written 4 days ago by
Ann
★ 2.4k
0
votes
0
replies
182
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 4 days ago by
Ram
43k • written 4 days ago by
mja
• 0
0
votes
0
replies
185
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
4 days ago by
Nitin
• 0
1
vote
5
replies
544
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Luka
• 0
0
votes
0
replies
185
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Ram
43k • written 4 days ago by
yifangt86
▴ 60
0
votes
0
replies
178
views
Chemical structure validation
structure
cap
validation
metabolite
4 days ago by
Rodolfo Adrián
• 0
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 4 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
0
votes
1
reply
256
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 4 days ago by
GenoMax
141k • written 4 days ago by
bioyas
▴ 10
0
votes
0
replies
201
views
Copy number variation plot
Copy-number-variation
genomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Emmi
• 0
1
vote
5
replies
685
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 4 days ago by
BioinfGuru
★ 1.7k • written 6 days ago by
rrehimi
• 0
0
votes
0
replies
173
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
4 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
277
views
Could you please assist in identifying this cluster?
single-cell
updated 4 days ago by
Ram
43k • written 5 days ago by
Kazo
• 0
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 5 days ago by
ATpoint
82k • written 7.1 years ago by
boymin2020
▴ 80
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 4 days ago by
ATpoint
82k • written 5 days ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
408
views
Plink merge errors.
cygwin64
bed
PLINK
5 days ago by
Dinmukhamed
• 0
0
votes
0
replies
192
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 4 days ago by
Ram
43k • written 5 days ago by
Dinmukhamed
• 0
0
votes
0
replies
190
views
miRDeep2: How to get the read counts
mirdeep2
5 days ago by
Atul K.
• 0
3
votes
4
replies
636
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
1 day ago by
rahu
• 0
0
votes
0
replies
198
views
Lncipedia GTF file error
Proteomics
updated 4 days ago by
Ram
43k • written 5 days ago by
atharvakarkare14
▴ 10
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 5 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
459
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
joe
▴ 510
0
votes
2
replies
529
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
5 days ago by
航太郎
• 0
0
votes
3
replies
481
views
Adding CB tag to bam file
samtools
bam
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
Maria
• 0
11
votes
12
replies
930
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 5 days ago by
Ram
43k • written 5 days ago by
iamsmor
• 0
0
votes
0
replies
208
views
create genewise sync file in popoolation
popoolation
updated 5 days ago by
GenoMax
141k • written 5 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
366
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
5 days ago by
Ashok
• 0
0
votes
2
replies
406
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
5 days ago by
Ashok
• 0
0
votes
0
replies
207
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 5 days ago by
Ram
43k • written 5 days ago by
samuelkalandarov2002
▴ 10
1
vote
1
reply
364
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
5 days ago by
otieno43
▴ 30
0
votes
2
replies
414
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
4 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
197
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
2 days ago by
Javier
• 0
1
vote
4
replies
674
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 5 days ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
0
replies
172
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
5 days ago by
enferdeflame
• 0
1
vote
1
reply
405
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 5 days ago by
Chris
▴ 260
0
votes
0
replies
183
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 5 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
3
votes
9
replies
779
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 6 days ago by
Elisabeth Gasteiger
★ 2.4k • written 6 days ago by
Jacky
• 0
0
votes
1
reply
262
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 6 days ago by
GenoMax
141k • written 6 days ago by
predeus
★ 1.9k
0
votes
1
reply
260
views
DEseq2
RNA-seq
DESeq2
updated 5 days ago by
Ram
43k • written 6 days ago by
rrehimi
• 0
1,000 results • Page
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Comment: How to trim transcripts using information from NCBI contamination screen report
Difference Between "Mate Pair" And "Pair-End"
Difference Between "Mate Pair" And "Pair-End"
Comment: To get p-values for the TPM
Comment: HaplotypeCaller - only SNPs
Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
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Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
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Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
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100k
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You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Windo…
Answer: Tax4Fun2 - error
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You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Win…
Comment: different FeatureCounts output for the same data
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141k
> featureCounts alignment rate is only around 15-20%. You mean assignment rate? It is that low even after allowing for counting of multi-m…
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141k
> 20386810 (88.67%) aligned concordantly exactly 1 time This result is fine.
Comment: To get p-values for the TPM
by
ATpoint
82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
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by
njornet
▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
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★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
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gv
• 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM
by
VITALA
• 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
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