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232 results • Page
1 of 5
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0
votes
0
replies
15
views
Plink merge errors.
merge
file
.bed
cygwin64
PLINK
1 hour ago by
Dinmukhamed
• 0
0
votes
1
reply
74
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
updated 2 hours ago by
BioinfGuru
★ 1.6k • written 14 hours ago by
Shicheng Guo
★ 9.4k
0
votes
3
replies
78
views
Mapping ortholog human and mouse transcript
biomart
2 hours ago by
1769mkc
★ 1.2k
0
votes
1
reply
42
views
How do I get the gene annotations as a text file from a genebank file?
genebank
sequence-annotation
updated 3 hours ago by
BioinfGuru
★ 1.6k • written 4 hours ago by
eae6d2e7
• 0
1
vote
1
reply
98
views
News:
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Vol…
systems_biology
endocrinology
machine_learning
ML
mathematical_modelling
updated 2 hours ago by
Mensur Dlakic
★ 26k • written 4 hours ago by
Johannes W. Dietrich
• 0
0
votes
0
replies
32
views
Alignment with new reference
alignment
5 hours ago by
marco.barr
▴ 30
0
votes
0
replies
33
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
8 hours ago by
pavithraashokkumar818
• 0
1
vote
1
reply
103
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
updated 8 hours ago by
Soheil
▴ 100 • written 20 hours ago by
sithlordashley
• 0
0
votes
0
replies
27
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
8 hours ago by
analyst
▴ 10
0
votes
0
replies
37
views
Convert to ENTREZGENE
maize
ENTREZGENE
11 hours ago by
sansan_96
▴ 50
1
vote
0
replies
45
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
13 hours ago by
Shicheng Guo
★ 9.4k
4
votes
9
replies
935
views
Error in openning FastQC
fastqc
igv
updated 15 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
0
votes
1
reply
100
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 16 hours ago by
Pierre Lindenbaum
160k • written 16 hours ago by
ekirsch
• 0
0
votes
4
replies
216
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
14 hours ago by
BRENO
• 0
0
votes
2
replies
133
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 15 hours ago by
Mensur Dlakic
★ 26k • written 18 hours ago by
Harrison
• 0
16
votes
10
replies
655
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 25 minutes ago by
Madelaine Gogol
5.3k • written 22 hours ago by
Ann
★ 2.4k
0
votes
0
replies
67
views
News:
Online course: Reproducibility in Bioinformatics
Singularity
Version-Control
Docker
Containers
updated 18 hours ago by
Ram
43k • written 18 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
59
views
News:
Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic
Bacterial-Genomics
Pangenomics
updated 18 hours ago by
Ram
43k • written 19 hours ago by
carlopecoraro2
★ 2.4k
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 19 hours ago by
Ram
43k • written 17 months ago by
Manav
• 0
0
votes
1
reply
130
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 20 hours ago by
Lissa Cruz Saavedra
• 0 • written 1 day ago by
SAsciences
• 0
0
votes
1
reply
81
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 20 hours ago by
GenoMax
140k • written 21 hours ago by
David Tachiquín
• 0
0
votes
9
replies
304
views
Low number of both surviving reads after trimming
trimmomatic
trimming
15 hours ago by
Jay
• 0
0
votes
2
replies
130
views
ONT direct RNA sequencing
DRS
ONT
updated 19 hours ago by
Ram
43k • written 1 day ago by
Karina
• 0
1
vote
2
replies
117
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
5 hours ago by
Mohamed Abderrahmane
▴ 10
3
votes
2
replies
120
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
22 hours ago by
DYLAN NICO
• 0
0
votes
2
replies
190
views
Can I have multiple active GDC download tokens?
TCGA
updated 22 hours ago by
Zhenyu Zhang
★ 1.1k • written 3 days ago by
mrk
• 0
0
votes
0
replies
71
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 22 hours ago by
Ram
43k • written 23 hours ago by
Tolga
▴ 20
0
votes
0
replies
66
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
23 hours ago by
alenew.am
• 0
0
votes
3
replies
361
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
22 hours ago by
Nitin
• 0
0
votes
1
reply
102
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 23 hours ago by
Ram
43k • written 23 hours ago by
chiditatawmbi
• 0
0
votes
1
reply
126
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 23 hours ago by
Ram
43k • written 1 day ago by
Picasa
▴ 640
0
votes
0
replies
85
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 22 hours ago by
Ram
43k • written 1 day ago by
udakshi
• 0
0
votes
0
replies
104
views
Training
chip-seq
ScATAC-seq
1 day ago by
Manhezz
• 0
1
vote
2
replies
143
views
Issue with making local BLAST database
R
mitochodrial
diatoms
blast
ncbi
updated 19 hours ago by
Ram
43k • written 1 day ago by
Begonia_pavonina
▴ 140
1
vote
1
reply
294
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
1 day ago by
Pierre Lindenbaum
160k
1
vote
2
replies
135
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 21 hours ago by
Ram
43k • written 1 day ago by
gdfsnkfns
• 0
1
vote
11
replies
315
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 20 hours ago by
GenoMax
140k • written 1 day ago by
Lila M
★ 1.2k
2
votes
2
replies
134
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 22 hours ago by
dariober
14k • written 1 day ago by
Pumla
• 0
0
votes
1
reply
101
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 19 hours ago by
Ram
43k • written 1 day ago by
Christian
• 0
2
votes
2
replies
150
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 1 day ago by
dthorbur
★ 1.7k • written 1 day ago by
Mohamed Abderrahmane
▴ 10
0
votes
0
replies
82
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
1 day ago by
Broccoli
• 0
0
votes
0
replies
78
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
1 day ago by
blur
▴ 280
0
votes
0
replies
93
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
1 day ago by
liuyibin2005
• 0
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 1 day ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
0
votes
0
replies
78
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 23 hours ago by
Ram
43k • written 1 day ago by
M'zelle
• 0
0
votes
5
replies
249
views
calculate mismatch rate from VCF file
mismatch-rate
VCF
updated 23 hours ago by
Ram
43k • written 1 day ago by
Dora
▴ 10
2
votes
4
replies
336
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
20 hours ago by
Lissa Cruz Saavedra
• 0
0
votes
0
replies
99
views
In scRNA, How should I set QC standards?
scRNA
QC
1 day ago by
mnx0723
• 0
0
votes
2
replies
257
views
Error occurs when migrate-n software performs "make mpis"
migrate-n
1 day ago by
lingxue
• 0
0
votes
0
replies
94
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
1 day ago by
Chris
▴ 260
232 results • Page
1 of 5
Recent Votes
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
F*up Night style events for Bioinformatics ? Comment if you're interested!
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Volume II
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
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Popular Question
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svlachavas
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160k
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Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Madelaine Gogol
5.3k
That sounds fun, and I've got some of these that I have told many people about (to keep them from making the same mistakes as me). I am pla…
Comment: Mapping ortholog human and mouse transcript
by
1769mkc
★ 1.2k
for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
Comment: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of
by
Mensur Dlakic
★ 26k
Take it from someone who has hosted both a successful and a failed research topic: these deadlines are unrealistic. I am guessing you are p…
Answer: Tissue specific mRNA expression dataset in human and mouse
by
BioinfGuru
★ 1.6k
Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy! The supplementary materials in the paper is…
Answer: Mapping ortholog human and mouse transcript
by
BioinfGuru
★ 1.6k
That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
Comment: Nanopore multisample variant calling
by
emilydolivo97
• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
Comment: How do I get the gene annotations as a text file from a genebank file?
by
BioinfGuru
★ 1.6k
Can you upload or post a link to the genbank file please?
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 100
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
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