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116,495 results • Page
1 of 2330
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1
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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
1 hour ago by
mathavanbioinfo
▴ 90
0
votes
1
reply
134
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 4 hours ago by
Ram
43k • written 8 hours ago by
Nina
• 0
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
1
vote
1
reply
140
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 5 hours ago by
Ram
43k • written 9 hours ago by
Giorgio
• 0
0
votes
0
replies
75
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 4 hours ago by
Ram
43k • written 10 hours ago by
Bioinformatician
• 0
0
votes
1
reply
154
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 10 hours ago by
GenoMax
141k • written 11 hours ago by
rebecca.calvo
• 0
0
votes
0
replies
104
views
Using samtools with GCS (google cloud storage) on docker a docker container seems to give "Protocol Not Supported" error
samtools
gcs
11 hours ago by
abhishekghadge
• 0
0
votes
3
replies
281
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 5 hours ago by
Ram
43k • written 12 hours ago by
rheab1230
▴ 140
1
vote
4
replies
382
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 11 hours ago by
Matthias Zepper
4.5k • written 13 hours ago by
Ann
★ 2.4k
0
votes
0
replies
86
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 13 hours ago by
Ram
43k • written 15 hours ago by
mja
• 0
0
votes
0
replies
96
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
15 hours ago by
Nitin
• 0
1
vote
5
replies
401
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 12 hours ago by
GenoMax
141k • written 15 hours ago by
Luka
• 0
0
votes
0
replies
102
views
absolute path for symbolic links in Snakefile
Snakemake
updated 15 hours ago by
Ram
43k • written 15 hours ago by
yifangt86
▴ 60
0
votes
0
replies
92
views
Chemical structure validation
structure
cap
validation
metabolite
15 hours ago by
Rodolfo Adrián
• 0
3
votes
8
replies
1.0k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 1 hour ago by
swbarnes2
14k • written 8 months ago by
bp22
▴ 80
0
votes
1
reply
161
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 15 hours ago by
GenoMax
141k • written 16 hours ago by
bioyas
▴ 10
0
votes
0
replies
110
views
Copy number variation plot
Copy-number-variation
genomics
updated 16 hours ago by
Ram
43k • written 17 hours ago by
Emmi
• 0
1
vote
5
replies
568
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 17 hours ago by
BioinfGuru
★ 1.7k • written 2 days ago by
rrehimi
• 0
0
votes
0
replies
95
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
17 hours ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
186
views
Could you please assist in identifying this cluster?
single-cell
updated 17 hours ago by
Ram
43k • written 18 hours 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 18 hours ago by
ATpoint
81k • written 7.1 years ago by
boymin2020
▴ 80
4
votes
11
replies
760
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 5 hours ago by
Ram
43k • written 20 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
329
views
Plink merge errors.
cygwin64
bed
PLINK
20 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
114
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 17 hours ago by
Ram
43k • written 20 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
115
views
miRDeep2: How to get the read counts
mirdeep2
22 hours ago by
Atul K.
• 0
1
vote
2
replies
386
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
rahu
• 0
0
votes
0
replies
124
views
Lncipedia GTF file error
Proteomics
updated 17 hours ago by
Ram
43k • written 1 day ago by
atharvakarkare14
▴ 10
7
votes
3
replies
2.7k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 1 day ago by
colindaven
6.3k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
316
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 1 hour ago by
swbarnes2
14k • written 1 day ago by
joe
▴ 510
0
votes
2
replies
430
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
1 day ago by
航太郎
• 0
0
votes
3
replies
341
views
Adding CB tag to bam file
samtools
bam
updated 1 hour ago by
swbarnes2
14k • written 1 day ago by
Maria
• 0
11
votes
12
replies
810
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 1 day ago by
Ram
43k • written 1 day ago by
iamsmor
• 0
0
votes
0
replies
137
views
create genewise sync file in popoolation
popoolation
updated 1 day ago by
GenoMax
141k • written 1 day ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
295
views
python file for coding potential calculator
cpc2.py
1 day ago by
Ashok
• 0
0
votes
2
replies
289
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
1 day ago by
Ashok
• 0
0
votes
2
replies
322
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
1 day ago by
Ashok
• 0
5
votes
2
replies
388
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 1 day ago by
shelkmike
★ 1.2k • written 2 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
142
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 1 day ago by
Ram
43k • written 1 day ago by
samuelkalandarov2002
• 0
1
vote
1
reply
298
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
1 day ago by
otieno43
▴ 30
0
votes
2
replies
338
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
17 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
146
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 1 day ago by
Ram
43k • written 1 day ago by
Javier
• 0
1
vote
4
replies
626
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 1 day ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
0
replies
142
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
1 day ago by
enferdeflame
• 0
0
votes
0
replies
154
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
1 day ago by
Chris
▴ 260
0
votes
0
replies
156
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
1
vote
9
replies
691
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 1 day ago by
Elisabeth Gasteiger
★ 2.4k • written 2 days ago by
Jacky
• 0
0
votes
1
reply
232
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 1 day ago by
GenoMax
141k • written 1 day ago by
predeus
★ 1.9k
0
votes
1
reply
245
views
DEseq2
RNA-seq
DESeq2
updated 1 day ago by
Ram
43k • written 1 day ago by
rrehimi
• 0
0
votes
0
replies
159
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
116,495 results • Page
1 of 2330
Recent Votes
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?
Answer: Cellranger count error: Input FASTQ file ended prematurely
Answer: RNA seq differential expression analysis
Answer: MEGA Analysis Issue on High-Performance Computer
Comment: Ciriquant not configuring hisat2 indexed files
bcftools multiple commands
bcftools pipe generated file from first command with second
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Recent Awards •
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Scholar
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Ann
★ 2.4k
Popular Question
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Rodolfo Adrián
• 0
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damian.szk
▴ 70
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alphaflylizard
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141k
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Recent Replies
Comment: Free/open source 23andme-like analysis
by
swbarnes2
14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
swbarnes2
14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
ATpoint
81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file
by
swbarnes2
14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2
by
Ram
43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
Answer: MEGA Analysis Issue on High-Performance Computer
by
Mensur Dlakic
★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
by
GenoMax
141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
rheab1230
▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Matthias Zepper
4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Normalized how?
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