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747 results • Page
4 of 15
Sort: Votes
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Views
Votes
Replies
3
votes
7
replies
574
views
Nextflow - How to pass the yml format input file from an argument to channel as a list
python
groovy
yaml
nextflow
12 days ago by
kani
▴ 10
3
votes
10
replies
2.3k
views
Salmon alignment based quantification
Salmon
rna-seq
quantification
updated 2 days ago by
Mat
▴ 60 • written 18 months ago by
edus_bioinfo
▴ 40
3
votes
5
replies
332
views
Does single end sequencing sequence both strands of the original fragment?
Illumina
sequencing
11 days ago by
Steven
▴ 20
3
votes
2
replies
1.0k
views
Contradiction in Harzard ratio and Log fold change
LogFC
Fold-change
Cancer
Hazard-Ratio
HR
updated 9 days ago by
Ram
40k • written 2.4 years ago by
Amir.Asgary
▴ 30
3
votes
3
replies
301
views
How to find variants in a specific gene in a cohort of 500k+ individuals?
variants
plink
SNPs
CNV
updated 19 days ago by
Pierre Lindenbaum
157k • written 19 days ago by
_quantum_girl_
▴ 10
3
votes
5
replies
852
views
News:
Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl
GTF
updated 12 days ago by
alejandrogzi
▴ 30 • written 10 months ago by
dlaehnemann
▴ 30
3
votes
1
reply
205
views
Automatic Cluster Annotation to the subsets of immune cells
singlecell
updated 8 days ago by
bk11
★ 1.2k • written 8 days ago by
synat.keam
▴ 80
3
votes
2
replies
469
views
Conflict between MAFFT and new PRANK installation
multiple-sequence-alignment
bash
prank
mafft
phylogenetics
updated 4 days ago by
Ram
40k • written 19 months ago by
noramarie
• 0
3
votes
4
replies
310
views
Visualization of multiple sequence alignment quality
blastp
blast
msa
updated 19 days ago by
GenoMax
134k • written 19 days ago by
dec986
▴ 370
3
votes
2
replies
219
views
HISAT2 Error
HISAT2
updated 14 days ago by
GenoMax
134k • written 14 days ago by
SHXVRR
▴ 20
3
votes
2
replies
289
views
Forum:
How to contribute to the next edition of Biostars Handbook
handbook
updated 17 days ago by
Ram
40k • written 17 days ago by
Fouad
▴ 20
3
votes
3
replies
425
views
Annovar doesnt output CADD scores
Annovar
CADD
updated 24 days ago by
Ram
40k • written 24 days ago by
AMARU
• 0
3
votes
7
replies
2.1k
views
Corrupted FASTq files with missing "+" under some sequences.
fastq
RNAseq
corruption
recover
updated 15 days ago by
Tommaso
• 0 • written 2.3 years ago by
akh22
▴ 90
3
votes
1
reply
1.2k
views
%% error in Rstudio
seurat
r
updated 2 days ago by
Ram
40k • written 2.1 years ago by
AbsaR
• 0
3
votes
5
replies
388
views
Ensembl site unresponsive in clusterProfiler analyses
parallell
clusterProfiler
R
updated 17 days ago by
manaswwm
▴ 440 • written 19 days ago by
enanoide
• 0
3
votes
2
replies
265
views
Scanning for ultra-hot topics in science via pubmed, or using other tools
growth
pubmed
3 days ago by
LauferVA
3.7k
3
votes
5
replies
509
views
Neither pysam nor samtools reading HTTPS-sourced BAM file correctly
bam
pysam
samtools
updated 21 days ago by
Istvan Albert
98k • written 23 days ago by
Alex Reynolds
35k
3
votes
2
replies
276
views
Could not view/find meta.data and Error merging three seurat object
Seurat
single-cell
updated 17 days ago by
Ram
40k • written 17 days ago by
synat.keam
▴ 80
3
votes
1
reply
2.8k
views
CWL bwa create index to bwa mem alignment workflow
Common-Workflow-Language
CWL
updated 13 days ago by
Ram
40k • written 6.1 years ago by
Biowoogles
▴ 20
3
votes
5
replies
387
views
Multiple sequence aligments - parallelisation
MSA
phylotranscriptomics
muscle
clustal
26 days ago by
Lada
▴ 30
3
votes
3
replies
283
views
Running python script in slurm using conda environment
slurm
python
conda
updated 12 days ago by
ATpoint
76k • written 12 days ago by
sidrah.maryam
▴ 50
3
votes
4
replies
363
views
Chromosome bias on RNA-Seq differential gene expression analysis
chromosome-bias
RNA-seq
2 days ago by
blz
▴ 30
3
votes
3
replies
316
views
About scdbfinder
scRNA-seq
doublets
scdbfinder
17 days ago by
Kazo
• 0
3
votes
4
replies
350
views
Weighted analysis
RNA-seq
6 days ago by
Peter
• 0
3
votes
3
replies
231
views
Issue with dbNSFP using SnpSift
dbNSFP
SnpSift
VCF
updated 27 days ago by
Ram
40k • written 27 days ago by
aidangcruickshank
▴ 10
3
votes
5
replies
419
views
Creating a Trinity assembly
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 27 days ago by
biofalconch
▴ 960 • written 28 days ago by
langziv
▴ 50
3
votes
5
replies
429
views
Optimal number of features to use when integrate multi samples by Seurat in scRNAseq
scRNASeq
Seurat
updated 23 days ago by
Ram
40k • written 23 days ago by
alwayshope
▴ 30
3
votes
4
replies
1.5k
views
Reference implementation rejects step without inputs
Common-Workflow-Language
cwl
updated 13 days ago by
Ram
40k • written 6.8 years ago by
unduthegun
• 0
3
votes
3
replies
397
views
Why is my genome assembly not aligning well?
alignment
13 days ago by
eennadi
▴ 30
3
votes
4
replies
383
views
How to Add Mutations to the sequence
mutations
NGS
sequence
updated 26 days ago by
Ram
40k • written 26 days ago by
Pratibha kadam
• 0
3
votes
6
replies
695
views
6 follow
Forum:
Is Bioinformatics a Professional Degree?
career
degree
25 days ago by
anasjamshed
▴ 120
3
votes
4
replies
365
views
Generate a fraction of immune cell between two condition from single cell RNAseq
single-cell
6 days ago by
synat.keam
▴ 80
3
votes
5
replies
1000
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio
purge_dups
Assembly
bionano
updated 10 days ago by
colindaven
5.5k • written 2.6 years ago by
pablo
▴ 280
3
votes
7
replies
593
views
GATK AnnotateVcfWithBamDepth returns zero DP for all variants in VCF
GATK
AnnotateVcfWithBamDepth
26 days ago by
ClkElf
▴ 50
3
votes
1
reply
183
views
What is the difference between norm --multiallelics -any versus --atomize?
bcftools
updated 4 days ago by
Ram
40k • written 4 days ago by
a615ebfb
▴ 30
3
votes
6
replies
426
views
Output FindMarkers()
seurat
27 days ago by
Chris
▴ 180
3
votes
2
replies
1.7k
views
Problems drawing cytobands with karyoploteR
RNA-Seq
R
Bioconductor
updated 24 days ago by
bernatgel
★ 3.4k • written 4.5 years ago by
uxiavb
▴ 10
3
votes
4
replies
318
views
Filtering VCF to divide with equal sizes
bcftools
vcf
updated 3 days ago by
Ram
40k • written 3 days ago by
avelarbio46
▴ 30
3
votes
10
replies
476
views
STAR index not working
STAR
RNA-Seq
3 days ago by
camillab.
▴ 130
3
votes
4
replies
418
views
During alignment STAR has stopped at started alignment step
STAR
updated 5 days ago by
Ram
40k • written 6 weeks ago by
Santhi
• 0
3
votes
2
replies
411
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 4 days ago by
yhdist
▴ 70 • written 7 days ago by
Cookin
• 0
3
votes
2
replies
1.7k
views
Extracting Residuals from Differential Expression Model
statistics
residuals
limma
updated 18 days ago by
Gordon Smyth
★ 6.4k • written 4.2 years ago by
JourneyToAbyss
▴ 210
3
votes
1
reply
272
views
Can I annotate a 32GB vcf file containing 300 samples at once using ANNOVAR?
ANNOVAR
written 18 days ago by
christinacanavati2014
• 0
2
votes
4
replies
368
views
join the control replicates
RNA-seq
updated 10 days ago by
seidel
11k • written 10 days ago by
Jean Pierre
• 0
2
votes
10
replies
4.4k
views
CWL: Getting the outputs(File) of a command line tool
Common-Workflow-Language
cwl
updated 13 days ago by
Ram
40k • written 6.4 years ago by
kevin.o.oluoch
▴ 70
2
votes
7
replies
1.4k
views
How to find newline character in fastq file? Is it essential to remove them?
FASTQ
updated 5 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
2
votes
2
replies
349
views
Currently lost between contigs, scaffolds and chromosomes due to positionally sorted scRNAseq bam files
bam
contigs
scRNAseq
updated 19 days ago by
ATpoint
76k • written 19 days ago by
nyxtoviopouli
• 0
2
votes
2
replies
259
views
Pangenome using Orthofinder
OrthoFinder
Pangenome
bacteria
7 days ago by
kirankumareripogu
▴ 10
2
votes
1
reply
218
views
bedGraphToBigWig: Missing Genome Coordinates
bamtobed
bed
5 days ago by
vanbelj
▴ 40
2
votes
4
replies
426
views
Help with celltype annotation
seurat
single-cell
8 days ago by
Chris
▴ 180
747 results • Page
4 of 15
Recent Votes
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
Comment: Hisat2 index and alignment question
Comment: Dotplot error: subscript out of bound
Comment: Dotplot : how to self-define the range of legend
Answer: Dotplot : how to self-define the range of legend
Convert SAM to BAM
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Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
swbarnes2
13k
G is the letter you get if there is no fluorescence. 75% of your reads have a lot of G. I don't think this run worked.
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Edoardo
• 0
I have 13,576 proteins in my file. I tried on a small set of 3 proteins and it worked fine!
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Mensur Dlakic
★ 24k
It should be faster, though you are not telling us how many proteins are in your query file. I suggest you use as many threads as availabl…
Comment: Hisat2 index and alignment question
by
Athena
• 0
That worked! Thank you. Didn't know that was an option... now I know.
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Edoardo
• 0
I ran blastp with the following command: blastp \ -db /path/to/Annotation_db/uniprot_fungi.fasta \ -query MYGEN.maker.output/…
Comment: Hisat2 index and alignment question
by
Athena
• 0
Pathway of my reference genome ![reference index pathway][1] when I tried running this command `hisat2 -p 8 -x /path/to/musculus_index…
Comment: Dotplot : how to self-define the range of legend
by
Xuhao
• 0
Thanks for your kind help.
Comment: Dotplot : how to self-define the range of legend
by
zau saa
▴ 50
add `breaks = c(-1, -0.5, 0, 0.5, 1)` to `scale_colour_gradientn()`
Comment: Dotplot : how to self-define the range of legend
by
Xuhao
• 0
It works!!! Thanks so much. Can I ask one more question? How to change the "average expression" scale into "-1, -0.5, 0, 0.5, 1"?
Comment: Low Alignment rate
by
dsull
★ 4.7k
Did you run FASTQC to check the quality of your sequencing samples? Otherwise, try taking some the reads that failed to align, and run the…
Comment: Integrated Seurat object change name of the two conditions
by
Amitm
★ 2.2k
Hi, See this [prev. post][1] where I contributed to, on accessing the meta data slot in a seurat object. There is more than one way. [1…
Comment: scRNAseq Differential expression analysis
by
jared.andrews07
★ 15k
I appreciate this statement and it largely mirrors my own. Lior sometimes makes extremely salient and important points. Other times, he's t…
Comment: Highly inflated p-values in GWAS by regenie
by
cwwong13
▴ 20
Thanks @4galaxy77 . The first 10 PCs were included in the calculation of the trait residuals, but still results were highly inflated.
Comment: Hisat2 index and alignment question
by
Istvan Albert
98k
the most logical and simple explanation is that most likely the path to index is specified incorrectly show us the paths with say `ls` the…
Comment: How to change from gene_id to GeneID/EntrezID using R
by
Kevin Blighe
86k
It would have been good if you had mentioned the species in your opening question. Regarding the fact that it may not be related to Ensembl…
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