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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
5
votes
10
replies
883
views
Error when viewing a bam file
samtools
updated 11 months ago by
Ram
44k • written 12 months ago by
Chris
▴ 280
5
votes
3
replies
565
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 8 months ago by
Ram
44k • written 8 months ago by
sarahmanderni
▴ 100
5
votes
4
replies
1.2k
views
Converting Bam file to Fasta (Zipped)
bedtools
samtools
updated 11 months ago by
Ram
44k • written 19 months ago by
Eliveri
▴ 350
5
votes
1
reply
694
views
Learning Linux advance commands
grep
awk
linux
sed
updated 7 months ago by
Zhitian Wu
▴ 60 • written 19 months ago by
rheab1230
▴ 140
5
votes
6
replies
1.8k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools
bam
bed
updated 11 months ago by
Ram
44k • written 18 months ago by
Eliveri
▴ 350
5
votes
5
replies
356
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
14 days ago by
Chris
▴ 280
5
votes
5
replies
7.3k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 5 weeks ago by
veldahan86
• 0 • written 3.9 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
10
replies
1.3k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
9 months ago by
alwayshope
▴ 40
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 6 weeks ago by
Ram
44k • written 6.5 years ago by
vikram
▴ 10
5
votes
5
replies
2.5k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 6 months ago by
Feng Tian
▴ 20 • written 5.6 years ago by
gewa
▴ 20
5
votes
2
replies
960
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 7 months ago by
yhdist
▴ 70 • written 8 months ago by
Cookin
▴ 10
5
votes
1
reply
1.9k
views
How does FindNeighbors() and FindClusters() related and work?
seurat
clustering
updated 9 months ago by
bk11
★ 2.5k • written 9 months ago by
leranwangcs
▴ 120
5
votes
8
replies
2.0k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 7 months ago by
Jingjingzhang
• 0 • written 3.8 years ago by
from the mountains
▴ 230
5
votes
11
replies
1.0k
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 9 months ago by
Ram
44k • written 9 months ago by
Chris
▴ 280
5
votes
8
replies
1.1k
views
sc-RNA seq pipeline
scRNA-seq
NGS
RNA-Seq
4 months ago by
Researcher
▴ 30
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 5 weeks ago by
Ram
44k • written 3.0 years ago by
Mat
▴ 60
5
votes
1
reply
704
views
Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance
vg
pggb
giraffe
updated 7 months ago by
Jordan M Eizenga
▴ 460 • written 7 months ago by
Kyran
▴ 30
5
votes
3
replies
1.0k
views
abyss-pe genome assembly
konnector
abyss-pe
updated 11 months ago by
Ram
44k • written 5.3 years ago by
Igor Lalin
• 0
5
votes
19
replies
4.1k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 4 months ago by
ATpoint
82k • written 5.0 years ago by
ta_awwad
▴ 340
5
votes
3
replies
665
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 6 months ago by
cmdcolin
★ 3.8k • written 6 months ago by
dariober
14k
5
votes
7
replies
877
views
About the value in bigwig file
ATAC-seq
updated 10 months ago by
rfran010
▴ 900 • written 10 months ago by
Chris
▴ 280
5
votes
6
replies
852
views
Calculate the percentage of genomic region covered from the BED file.
NGS
sequencing
genomics
exome
genes
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
adarsh_pp
▴ 40
5
votes
7
replies
994
views
Salmon index not progressing
salmon
updated 8 months ago by
Michael
54k • written 8 months ago by
camillab.
▴ 160
5
votes
1
reply
651
views
Enricher with Gene Symbols
DGE
ClusterProfiler
Enrich
ORA
updated 9 months ago by
bk11
★ 2.5k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
5
replies
565
views
Example MAF Files
MAF
updated 5 months ago by
Ram
44k • written 5 months ago by
anasjamshed
▴ 120
5
votes
4
replies
1.7k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 11 months ago by
Ram
44k • written 7.8 years ago by
statfa
▴ 760
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 7 months ago by
Istvan Albert
100k • written 5.9 years ago by
chris.bird
▴ 10
5
votes
3
replies
444
views
samtools view: error reading file
samtools
bowtie2
updated 10 weeks ago by
bioinfo_ga
▴ 70 • written 11 weeks ago by
ray
• 0
5
votes
8
replies
671
views
Multiple threads on ubuntu server
Ubuntu
updated 4 months ago by
colindaven
6.4k • written 4 months ago by
oghzzang
▴ 50
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 6 weeks ago by
Ram
44k • written 6.6 years ago by
firestar
★ 1.6k
5
votes
35
replies
3.8k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 10 months ago by
Jordan M Eizenga
▴ 460 • written 11 months ago by
anivlete
• 0
5
votes
5
replies
671
views
Counting 705 fasta header characters ('>') in human genome
human-genome
genetics
updated 7 months ago by
ATpoint
82k • written 7 months ago by
10mz1
▴ 10
5
votes
7
replies
541
views
RNA seq analysis
DESeq
RNA-seq
6 days ago by
Jacek
▴ 20
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 10 months ago by
Jordan M Eizenga
▴ 460 • written 16 months ago by
TN
• 0
5
votes
4
replies
750
views
FASTQ to BAM to CRAM to FASTQ
Samtools
6 months ago by
ManuelDB
▴ 80
5
votes
6
replies
1.4k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2
R
RNA-Seq
updated 11 months ago by
Ram
44k • written 4.1 years ago by
Ranan Jyoti Sarma
▴ 90
5
votes
6
replies
465
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 7 weeks ago by
Istvan Albert
100k • written 7 weeks ago by
Pumla
• 0
5
votes
11
replies
1.4k
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 9 months ago by
cmdcolin
★ 3.8k • written 9 months ago by
pablo
▴ 300
5
votes
5
replies
609
views
Generate BED file
bed
3 months ago by
daffodil
▴ 10
4
votes
6
replies
2.2k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by
Ram
44k • written 9.1 years ago by
Harish Sanja
▴ 10
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny
genome
alignment
updated 11 months ago by
Ram
44k • written 4.9 years ago by
Kumar
▴ 120
4
votes
4
replies
536
views
Correlation for ATAC-Seq and Chip-Seq
RNA-Seq
Chip-Seq
ATAC-Seq
12 weeks ago by
qudrat.nii
▴ 10
4
votes
2
replies
594
views
Can I still remove ambient RNA if I do not have raw barcode-gene matrix?
SoupX
7 months ago by
malonzm1
▴ 20
4
votes
12
replies
7.9k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 3 months ago by
mgdrnl
▴ 10 • written 3.4 years ago by
whb
▴ 60
4
votes
4
replies
829
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 11 months ago by
Joe
21k • written 12 months ago by
antoine.fauchois92
▴ 20
4
votes
14
replies
1.2k
views
remove white space in fastq file
fastq
updated 5 months ago by
GenoMax
142k • written 5 months ago by
gkarere
• 0
4
votes
5
replies
809
views
Does adding reads cause batch effects?
kallisto
RNAseq
11 months ago by
bioinfo
▴ 150
4
votes
2
replies
697
views
Visualization package for Maf Files using Python
Python
maftools
Visualization
MAF
updated 7 months ago by
Mark
★ 1.5k • written 7 months ago by
Manuel Sokolov Ravasqueira
▴ 100
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV
WGS
updated 11 months ago by
Ram
44k • written 6.8 years ago by
zhang248
▴ 40
4
votes
8
replies
636
views
GCP Snakemake
snakemake
GCP
updated 3 months ago by
Ram
44k • written 3 months ago by
Fadwa
▴ 10
1,000 results • Page
2 of 20
Recent Votes
GO analysis: Different results EnrichGO vs ShinyGO
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
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Recent Awards •
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▴ 150
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
Yes please see below: TraesCS2B02G372900 TraesCS2B02G375100 TraesCS2B02G374700 TraesCS2B02G382000
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Thanks for your answer, but as far as I know, gProfiler2 does not support bacteria. Could you please suggest alternative websites or softwa…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi Alex, I'm sorry if I wasn't initially clear! The question hasn't changed; I had written in this post that I wanted all pairwise combinat…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
• 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
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