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116,046 results • Page
1 of 2321
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0
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52
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Help with summarizeOverlaps function in RNASeq analysis using R
R
RNA-Seq
summarizeOverlaps
GenomicAlignments
updated 2 hours ago by
Soheil
▴ 100 • written 5 hours ago by
FJCF
• 0
0
votes
0
replies
32
views
Data table for LOEUF loss-of-function observed/expected upper bound fraction
LOEUF
4 hours ago by
Shicheng Guo
★ 9.4k
794
votes
167
replies
139k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.6k • written 7.3 years ago by
Istvan Albert
100k
0
votes
0
replies
35
views
cell type adjustment - how many cell types to include?
celltypes
ewas
4 hours ago by
kaybelter
• 0
0
votes
0
replies
41
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
cgi
models
gene
translation
gif
4 hours ago by
O.rka
▴ 710
0
votes
0
replies
36
views
details about PCA in plink 2.0: eigenvectors, PCs, scores
gwas
plink
pca
4 hours ago by
kaybelter
• 0
1
vote
2
replies
86
views
Database for non cancer cell lines
cell-line
L1000
rna-seq
cancer-database
LINCS
3 hours ago by
ANSARAHMAD
• 0
2
votes
2
replies
153
views
Convert to ENTREZGENE
maize
ENTREZ
5 hours ago by
sansan_96
▴ 50
0
votes
1
reply
79
views
How to calculate depth of coverage and applying read depth filter
Depth-of-Coverage
CRAM
WGS
updated 5 hours ago by
Ram
43k • written 8 hours ago by
prds
• 0
1
vote
3
replies
110
views
BioGRID REST - How to retrieve all the protein interactions?
BioGRID
Python
REST
updated 8 hours ago by
Pierre Lindenbaum
160k • written 9 hours ago by
dbykov
• 0
4
votes
4
replies
156
views
Problem generating paired end reads when converting Cell Ranger's BAM result to FASTQ
fastq
bam
4 hours ago by
ntuzov
• 0
0
votes
0
replies
53
views
Finding chimeric reads for CRISPR edited mouse cells from RNA-Seq data
RNA-seq
crispr
updated 5 hours ago by
Ram
43k • written 9 hours ago by
Ethan
• 0
2
votes
2
replies
134
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
5 hours ago by
I0110
▴ 140
0
votes
0
replies
56
views
RSEM: Error: reads file does not look like a FASTQ file
FASTQ
RSEM
updated 10 hours ago by
GenoMax
140k • written 10 hours ago by
Mohamed Abderrahmane
▴ 10
0
votes
0
replies
77
views
Plink merge errors.
cygwin64
bed
PLINK
updated 10 hours ago by
Ram
43k • written 13 hours ago by
Dinmukhamed
• 0
0
votes
1
reply
156
views
Tissue specific mRNA expression dataset in human and mouse
tissue-specificity
updated 8 hours ago by
Ram
43k • written 1 day ago by
Shicheng Guo
★ 9.4k
1
vote
3
replies
187
views
Mapping ortholog human and mouse transcript
biomart
14 hours ago by
1769mkc
★ 1.2k
0
votes
3
replies
194
views
How do I get the gene annotations as a text file from a genbank file?
sequence-annotation
genbank
updated 7 hours ago by
Ram
43k • written 16 hours ago by
eae6d2e7
• 0
3
votes
2
replies
297
views
News:
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Vol…
mathematical-modelling
endocrinology
ML
systems-biology
machine-learning
10 hours ago by
Johannes W. Dietrich
• 0
0
votes
1
reply
124
views
Alignment with new reference
alignment
updated 11 hours ago by
GenoMax
140k • written 17 hours ago by
marco.barr
▴ 30
0
votes
0
replies
78
views
Bowtie2 alignment rate
galaxy
Bowtie
alignment-rate
updated 10 hours ago by
Ram
43k • written 20 hours ago by
pavithraashokkumar818
• 0
1
vote
1
reply
164
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
updated 20 hours ago by
Soheil
▴ 100 • written 1 day ago by
sithlordashley
• 0
0
votes
0
replies
78
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
21 hours ago by
analyst
▴ 10
1
vote
0
replies
81
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
1 day ago by
Shicheng Guo
★ 9.4k
4
votes
9
replies
969
views
Error in openning FastQC
fastqc
igv
updated 1 day ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
0
votes
2
replies
158
views
vcf file: number of samples does not match number of columns
vcf
bcftools
8 hours ago by
ekirsch
• 0
0
votes
4
replies
274
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
1 day ago by
BRENO
• 0
0
votes
5
replies
269
views
Error running local blastn in R using system2
blastn
NCBI
R
11 hours ago by
Harrison
• 0
16
votes
10
replies
749
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 12 hours ago by
Madelaine Gogol
5.3k • written 1 day ago by
Ann
★ 2.4k
0
votes
0
replies
87
views
News:
Online course: Reproducibility in Bioinformatics
Singularity
Version-Control
Docker
Containers
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
75
views
News:
Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic
Bacterial-Genomics
Pangenomics
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.4k
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 1 day ago by
Ram
43k • written 17 months ago by
Manav
• 0
0
votes
1
reply
147
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 1 day ago by
Lissa Cruz Saavedra
• 0 • written 1 day ago by
SAsciences
• 0
0
votes
1
reply
99
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 1 day ago by
GenoMax
140k • written 1 day ago by
David Tachiquín
• 0
0
votes
9
replies
328
views
Low number of both surviving reads after trimming
trimmomatic
trimming
1 day ago by
Jay
• 0
0
votes
2
replies
148
views
ONT direct RNA sequencing
DRS
ONT
updated 1 day ago by
Ram
43k • written 1 day ago by
Karina
• 0
2
votes
4
replies
215
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
11 hours ago by
Mohamed Abderrahmane
▴ 10
3
votes
2
replies
149
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
1 day ago by
DYLAN NICO
• 0
0
votes
2
replies
207
views
Can I have multiple active GDC download tokens?
TCGA
updated 1 day ago by
Zhenyu Zhang
★ 1.1k • written 4 days ago by
mrk
• 0
0
votes
0
replies
90
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 1 day ago by
Ram
43k • written 1 day ago by
Tolga
▴ 20
0
votes
0
replies
83
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
1 day ago by
alenew.am
• 0
0
votes
3
replies
398
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
1 day ago by
Nitin
• 0
0
votes
1
reply
130
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
chiditatawmbi
• 0
0
votes
1
reply
145
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 1 day ago by
Ram
43k • written 1 day ago by
Picasa
▴ 640
0
votes
0
replies
100
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 1 day ago by
Ram
43k • written 1 day ago by
udakshi
• 0
0
votes
0
replies
125
views
Training
chip-seq
ScATAC-seq
1 day ago by
Manhezz
• 0
1
vote
2
replies
159
views
Issue with making local BLAST database
R
mitochodrial
diatoms
blast
ncbi
updated 1 day ago by
Ram
43k • written 1 day ago by
Begonia_pavonina
▴ 140
1
vote
1
reply
312
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
1 day ago by
Pierre Lindenbaum
160k
1
vote
2
replies
153
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 1 day ago by
Ram
43k • written 1 day ago by
gdfsnkfns
• 0
1
vote
11
replies
330
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 1 day ago by
GenoMax
140k • written 1 day ago by
Lila M
★ 1.2k
116,046 results • Page
1 of 2321
Recent Votes
C: Plotting heatmap of Marker genes in each celltypes in Seurat
C: Plotting heatmap of Marker genes in each celltypes in Seurat
A: Plotting heatmap of Marker genes in each celltypes in Seurat
C: Plotting heatmap of Marker genes in each celltypes in Seurat
C: Plotting heatmap of Marker genes in each celltypes in Seurat
Plotting heatmap of Marker genes in each celltypes in Seurat
Comment: Problem generating paired end reads when converting Cell Ranger's BAM result to
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★ 1.7k
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Recent Replies
Answer: Help with summarizeOverlaps function in RNASeq analysis using R
by
Soheil
▴ 100
I'm guessing you are trying to get the gene expression counts from your BAM files. In this case, I suggest using **featureCounts** from the…
Comment: Database for non cancer cell lines
by
ANSARAHMAD
• 0
Thanks for your response, i will try this method
Comment: Problem generating paired end reads when converting Cell Ranger's BAM result to
by
ATpoint
81k
SRA uses its own nomenclature, while CellRanger reads the original file names. Thats my guess. bamtofastq is save to use, continue with ret…
Answer: Database for non cancer cell lines
by
Trivas
★ 1.7k
NCBI GEO has started generating RNA-seq counts for publicly deposited RNA-seq studies and GEO2R (see https://www.ncbi.nlm.nih.gov/geo/geo2r…
Comment: Convert to ENTREZGENE
by
sansan_96
▴ 50
Kevin, thank you very much for your valuable help. I am using this output for a KEGG analysis, although I recover very few genes for my ana…
Comment: Can any JBrowse2 tracks show multiple colors for reads at different nucleotide p
by
I0110
▴ 140
Thanks for your reply, I add the description for data input in the text.
Comment: Problem generating paired end reads when converting Cell Ranger's BAM result to
by
ntuzov
• 0
Thanks for replying. I ran it, but then there is one more question about bamtofastq output (see above).
Comment: Hybrid assembly Pacbio- Nanopore
by
colindaven
6.3k
48m is tiny, fungal size maybe. HiFi alone should be completely fine. You may not need PoreC on top of that. Start simple and integrate fur…
Comment: Nanopore multisample variant calling
by
colindaven
6.3k
There was some discussion with others here https://github.com/WGLab/NanoCaller/issues/21, but I never found an adequate solution - actually…
Comment: Problem generating paired end reads when converting Cell Ranger's BAM result to
by
swbarnes2
14k
There's no point in separating lanes 1 and 2. It's fine if they are combined.
Answer: Convert to ENTREZGENE
by
Kevin Blighe
87k
Hello, There is an annotation table for corn / maize (*Zea mays*) at ensembl, accessible via *biomaRt*. What I would do is to first pull …
Comment: How do I get the gene annotations as a text file from a genbank file?
by
Ram
43k
This question was also asked on bioinfo SE: https://bioinformatics.stackexchange.com/questions/22331/how-do-i-get-the-gene-annotations-as-a…
Comment: error when running phg create-maf-vcf to build a built practical haplotype graph
by
lcj34
▴ 410
FYI - phgv2 version Release 2.2.68.117 has the updated BioKotlin release with this fix.
Answer: How to calculate depth of coverage and applying read depth filter
by
ATpoint
81k
You can do that with https://github.com/brentp/mosdepth as a starting point and then postprocess the output.
Comment: Piping samtools to R
by
joe
▴ 470
I actually found this to be <s>bad</s> (outdated?) advice. I had no problem to pipe the output of samtools mpileup into an Rscript (R > 4.1…
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