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764 results • Page
3 of 16
Sort: replies
Rank
Views
Votes
Replies
2
votes
7
replies
680
views
VG mapping paired-end reads: error [xg]: multiple hits for XXX
variation-graph
reads
pangenome
vg
paired-end
21 days ago by
nkls063408
• 0
8
votes
7
replies
2.4k
views
6 follow
LncRNA Differential Expression and Analysis of lncRNA and mRNA co-expression.
RNA-Seq
alignment
co-expression
lncRNA
DESeq2
updated 24 days ago by
AS-git
• 0 • written 5.0 years ago by
conor93
▴ 70
6
votes
7
replies
1.2k
views
wc -l or wc -c which linux command is best to find total read count in fastq file?
linux
updated 6 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
2
votes
7
replies
1.4k
views
How to find newline character in fastq file? Is it essential to remove them?
FASTQ
updated 6 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
0
votes
7
replies
784
views
Mugsy error -directory must be a directory
Mugsy
updated 3 days ago by
Ram
40k • written 2.8 years ago by
A_heath
▴ 140
5
votes
7
replies
540
views
Can one sample t.test be used to determine statistical significance for log2FC values?
log2FC
T.test
updated 25 days ago by
dsull
★ 4.7k • written 26 days ago by
aUser
▴ 30
8
votes
7
replies
1.2k
views
Whole genome species clustering
phylogeny
assembly
phylogenetics
updated 26 days ago by
pmiller
• 0 • written 2.4 years ago by
robert.murphy
▴ 80
0
votes
7
replies
734
views
Converting string to numerical in bcftools
bcftools
updated 27 days ago by
AMARU
• 0 • written 10 weeks ago by
pjuge
• 0
5
votes
7
replies
465
views
Elusive syntax error in Snakefile
snakemake
updated 5 days ago by
Ram
40k • written 6 days ago by
Giuseppe Giovanni
▴ 30
4
votes
7
replies
722
views
How to subtract a number from protein IDs?
blast
updated 3 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
0
votes
7
replies
2.7k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 10 days ago by
Ram
40k • written 5.3 years ago by
AP
▴ 80
0
votes
7
replies
184
views
how to identify uniq genes between two gff files.
Genes
Uniq
Annotation
GFF
21 minutes ago by
nikhil
▴ 10
3
votes
7
replies
550
views
Identifying transcription factors for a list of genes
transcription-factor
updated 27 days ago by
Yogi
▴ 10 • written 28 days ago by
lbombini
• 0
8
votes
7
replies
2.3k
views
CWL rerunning completed output
Common-Workflow-Language
CWL
updated 13 days ago by
Ram
40k • written 6.1 years ago by
bruce.moran
▴ 950
5
votes
6
replies
375
views
From where can I obtain vcf files of healthy exomes
exome
VCF
updated 20 days ago by
Ram
40k • written 20 days ago by
christinacanavati2014
• 0
7
votes
6
replies
10k
views
7 follow
Blastn Segmentation Fault
blast
updated 19 days ago by
Amirhossein Hajianpour
▴ 40 • written 11.8 years ago by
Srihari
▴ 30
9
votes
6
replies
1.2k
views
6 follow
Forum:
GTF files from Ensembl Releases 105 and 106 unsorted
Ensembl
bug
GTF
updated 12 days ago by
ATpoint
76k • written 10 months ago by
dlaehnemann
▴ 30
6
votes
6
replies
436
views
Integration in single cell RNAseq: What does it mean?
Single
cell
updated 25 days ago by
Chris
▴ 180 • written 26 days ago by
synat.keam
▴ 80
0
votes
6
replies
867
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
4 days ago by
ccbb7aab4
▴ 20
0
votes
6
replies
947
views
How to run delly with multi-threading mode?
SV
calling
delly
updated 5 days ago by
bio-jr
▴ 10 • written 8 months ago by
Xi
• 0
1
vote
6
replies
588
views
Found some plasmids in my sequence. IS there any tool or process by which i can find whether there are any AMR genes within those sequence?
WGS
updated 26 days ago by
Ram
40k • written 27 days ago by
Mustafa
• 0
7
votes
6
replies
524
views
Best practices scRNA-seq guide for beginer
scRNA-seq
eBook
23 days ago by
octpus616
▴ 80
3
votes
6
replies
460
views
summarize consecutive columns over a data frame
tidyverse
r
offtopic
updated 2 days ago by
Ram
40k • written 14 days ago by
Assa Yeroslaviz
★ 1.8k
8
votes
6
replies
522
views
Short Read Data Genome Assembly
spades
genome-assembly
updated 15 days ago by
ccstaats
▴ 30 • written 19 days ago by
Umer
▴ 50
4
votes
6
replies
2.6k
views
IDT vs primer 3 - PCR dimerisation
PCR
primer3
IDT
primer
updated 10 days ago by
Emrah
• 0 • written 3.1 years ago by
timothy.kirkwood
▴ 130
2
votes
6
replies
396
views
Read block operation failed with BAM file
bgzip
samtools
bam
pysam
htslib
6 days ago by
Alex Reynolds
35k
1
vote
6
replies
552
views
How to use the Combat-seq for batch effect removal?
batch-effect
normalization
Combat-seq
updated 27 days ago by
Ram
40k • written 28 days ago by
Yoomi
• 0
2
votes
6
replies
489
views
Installing ensemble VEP by running INSTALL.pl takes too long.
Ensembl
VEP
updated 17 days ago by
Ben_Ensembl
★ 2.3k • written 18 days ago by
lsy9
▴ 20
6
votes
6
replies
5.3k
views
How is logFC and p-value estimated (for volcano plots)?
R
edgeR
fold-Change
updated 10 days ago by
Ram
40k • written 6.5 years ago by
LRStar
▴ 200
3
votes
6
replies
699
views
6 follow
Forum:
Is Bioinformatics a Professional Degree?
career
degree
25 days ago by
anasjamshed
▴ 120
8
votes
6
replies
632
views
Problems using ERCC spike-ins for normalization in DESeq2
Spike-ins
Differential-expression
DESeq2
RNA-seq
13 days ago by
manuel.fernandez
▴ 40
7
votes
6
replies
3.2k
views
CWL: word counting
Common-Workflow-Language
cwl
updated 13 days ago by
Ram
40k • written 6.3 years ago by
gultagr
▴ 10
0
votes
6
replies
542
views
How to get top 10 genes expressed in a cluster ( for cell type identification)?
seurat
11 days ago by
Chris
▴ 180
1
vote
6
replies
3.2k
views
Extracting sequence, not reads, by position from bam
sequence
updated 5 days ago by
manu
• 0 • written 5.0 years ago by
geneware
▴ 10
3
votes
6
replies
430
views
Output FindMarkers()
seurat
27 days ago by
Chris
▴ 180
3
votes
6
replies
637
views
BWA | SAMtools | GATK debugging help
alignment
mapping
vcf
12 days ago by
TheScriptOfGilgamesh
▴ 20
0
votes
6
replies
525
views
A cluster expresses two types of cells' markers in scRNA-seq
scRNA-seq
annotate
27 days ago by
feather-W
• 0
1
vote
6
replies
569
views
Batch correction in DESeq2 - limited impact for unsupervised downstream analyses
deseq2
13 days ago by
Jane
• 0
2
votes
5
replies
382
views
Centrality analysis to identify TFs
TF
updated 24 days ago by
biofalconch
▴ 960 • written 25 days ago by
Chris
▴ 180
4
votes
5
replies
436
views
Recapitulating a GenomeBrowser-style plot
IGV
genome-browser
29 days ago by
LChart
3.3k
4
votes
5
replies
582
views
Help with error scanpy
scanpy
11 days ago by
Chris
▴ 180
2
votes
5
replies
443
views
Uniprot Database for download
proteomics
Uniprot
updated 4 days ago by
Elisabeth Gasteiger
★ 2.3k • written 4 weeks ago by
SHN
▴ 40
1
vote
5
replies
1.4k
views
--preserve_environment with docker containers?
cwltool
Common-Workflow-Language
cwl
updated 13 days ago by
Ram
40k • written 6.0 years ago by
Biowoogles
▴ 20
2
votes
5
replies
380
views
Extract only insecta information from Blast nr DB.
Blast
updated 14 days ago by
GenoMax
134k • written 14 days ago by
wldud0915ek
• 0
2
votes
5
replies
535
views
How to distinguish between normal and malignant epithelial cells based on CNV?
scRNA-seq
r
CNV
infercnv
CNA
updated 13 days ago by
LChart
3.3k • written 18 days ago by
fifty_fifty
▴ 60
2
votes
5
replies
234
views
How to change from gene_id to GeneID/EntrezID using R
identifiers
Deseq2
GeneID
updated 5 hours ago by
Kevin Blighe
86k • written 1 day ago by
Nicolas
• 0
1
vote
5
replies
951
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx
differential-expression
t-test
deconvolution
13 days ago by
Sam
▴ 290
3
votes
5
replies
388
views
Ensembl site unresponsive in clusterProfiler analyses
parallell
clusterProfiler
R
updated 18 days ago by
manaswwm
▴ 440 • written 19 days ago by
enanoide
• 0
7
votes
5
replies
485
views
Is there a benchmark analysis for the best tool for multiome single-cell RNA+ATAC data analysis?
multiome
single-cell
updated 11 days ago by
ATpoint
76k • written 12 days ago by
Dan
▴ 140
3
votes
5
replies
423
views
Creating a Trinity assembly
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 28 days ago by
biofalconch
▴ 960 • written 29 days ago by
langziv
▴ 50
764 results • Page
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Comment: Integrated Seurat object change name of the two conditions
Concatenating fastq.gz files across lanes
A: Concatenating fastq.gz files across lanes
Answer: bedGraph for Coverage of Insert from Paired-End Data?
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
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Answer: Filter transcription factors
by
jared.andrews07
★ 15k
[This database](http://humantfs.ccbr.utoronto.ca/download.php) has been the best I've found.
Comment: Filter transcription factors
by
Ram
40k
What have you tried? Have you looked at GO annotations?
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
yes @juke34 , I tried agat_sp_compare_two_annotations.pl for both gff files and got comparative output in table format. Thank you very muc…
Comment: Integrated Seurat object change name of the two conditions
by
Amitm
★ 2.2k
Yes, its similar structure. This snippet should add a new metadata column "sample.New" with what you want to do # Assuming a seurat obj. c…
Comment: Low Alignment rate
by
biofalconch
▴ 960
Yeap, you can sample your reads with `seqtk` like this: seqtk sample -s100 read2.fq 100 > Sample.fq Take a couple and run them throug…
Answer: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★ 1.2k
You won't find them on circBase. circAtlas has the mature spliced sequence available. You can [search for circRNAs](https://ngdc.cncb.a…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
Ram
40k
\#TIL mambaforge - better than continuum's conda images I'm guessing?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
arriyaz.nstu
▴ 30
If the laptop doesn't support WSL2, then will the Docker (with linux) work?
Comment: Integrated Seurat object change name of the two conditions
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camillab.
▴ 130
thanks but my metadata looks different from yours. Will it work even there are not the same "structure"? or…
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by
ATpoint
76k
Docker is great, I use it daily since you're independent of the host computer and can share and pull the images via DockerHub. It's also gr…
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ATpoint
76k
If you do DE analysis on single-cell level then I find it critical to enforce some cutoff, as many cells means a lot of power so you get ev…
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Did you google "visualize BED file on genome"?<a href="" title="Text added because biostars parser needs it"></a>
Comment: obtaining circular RNAs' sequences from circBase
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Ram
40k
> as you know No I did not. I know this is a cultural mannerism but it's antiquated. Please abandon this phrase, it can come across as con…
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
omer.shomrat
• 0
Thanks a lot for the response! I'm doing pathway enrichment analysis (using clusterProfiler) on almost all genes in each cluster, with the…
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by
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40k
Ah I missed the part where DNANexus makes this problem out of our reach. Thank you, GenoMax!
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