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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
7
votes
12
replies
1.7k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome
bwa
bash
updated 6 months ago by
Ram
43k • written 4.2 years ago by
Karma
▴ 310
2
votes
12
replies
1.7k
views
gatk Funcotator
vcf
Funcotator
gatk
10 months ago by
Saurabh
• 0
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 5 weeks ago by
Ram
43k • written 5.6 years ago by
c.clarido
▴ 110
2
votes
12
replies
1.6k
views
scrna seq analysis - doublets
scrna
seq
code
r
updated 10 months ago by
Nitin Narwade
★ 1.6k • written 10 months ago by
bioinformatics
▴ 40
3
votes
12
replies
971
views
why 99% reads failed to align in mir-seq analysis?
Fastqc
bowtie1
miRNA-seq
alignment
differential-expression-analysis
3 months ago by
mohammadhassanj
▴ 260
0
votes
12
replies
3.3k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 11 months ago by
Ram
43k • written 6.5 years ago by
fonteneaudam
▴ 20
3
votes
12
replies
580
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
4 weeks ago by
Lila M
★ 1.2k
0
votes
12
replies
2.5k
views
Differential gene expression analysis with no replicates using edgeR
edgeR
RNA-seq
DEG
updated 4 months ago by
Sajad
▴ 90 • written 17 months ago by
Apex92
▴ 280
1
vote
11
replies
1.2k
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 7 months ago by
GenoMax
142k • written 8 months ago by
langziv
▴ 50
0
votes
11
replies
1.2k
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
7 months ago by
evmae
• 0
2
votes
11
replies
814
views
Reference Guided genome assembly
tabix
updated 10 weeks ago by
Michael
54k • written 10 weeks ago by
sainavyav22
• 0
5
votes
11
replies
1.4k
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 8 months ago by
cmdcolin
★ 3.8k • written 9 months ago by
pablo
▴ 300
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by
Kevin Blighe
87k • written 8 months ago by
Michelle Guerra
• 0
0
votes
11
replies
1.6k
views
count file having zero
RNA-Seq
next-gen
alignment
updated 10 months ago by
Ram
43k • written 5.3 years ago by
BioBaby
▴ 20
5
votes
11
replies
1.0k
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 9 months ago by
Ram
43k • written 9 months ago by
Chris
▴ 260
4
votes
11
replies
1.6k
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
updated 6 months ago by
Brian Bushnell
20k • written 8 months ago by
Y
• 0
4
votes
11
replies
678
views
Remove X in row name with only number
GSVA
updated 12 weeks ago by
Ram
43k • written 12 weeks ago by
Chris
▴ 260
0
votes
11
replies
813
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 7 weeks ago by
barslmn
★ 2.1k • written 8 weeks ago by
avelarbio46
▴ 30
2
votes
11
replies
5.2k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 3 months ago by
e.r.zakiev
▴ 210 • written 7.8 years ago by
CAnna
▴ 20
2
votes
11
replies
1.1k
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
5 months ago by
sil_bioinfo
▴ 40
0
votes
11
replies
2.3k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 10 months ago by
Ram
43k • written 5.0 years ago by
saumya.sharma1509
• 0
0
votes
11
replies
616
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
8 days ago by
atowns21
• 0
0
votes
10
replies
1.0k
views
ONT Raw Read Sequencing Pipeline
remora
dorado
ONT
Basecall
3 months ago by
turcoa1
• 0
1
vote
10
replies
1.0k
views
file conversion from gtf to gff3 for evidence modeler
gff3
stringtie
gtf
6 months ago by
rj.rezwan
• 0
0
votes
10
replies
516
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 4 days ago by
i.sudbery
19k • written 12 days ago by
Patadu94
• 0
0
votes
10
replies
896
views
Problem running scPred
scPred
scPredict
updated 7 weeks ago by
Ram
43k • written 4 months ago by
Nitin
• 0
1
vote
10
replies
1.2k
views
Coverage histogram query
Alignment
8 months ago by
prasundutta87
▴ 660
0
votes
10
replies
678
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
4 weeks ago by
dzisis1986
▴ 70
8
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
10 months ago by
yoshifumimiya
▴ 40
3
votes
10
replies
1.2k
views
STAR index not working
STAR
RNA-Seq
7 months ago by
camillab.
▴ 160
1
vote
10
replies
1.2k
views
Do monoclonal antibodies have a blocking effect?
block
antibody
offtopic
updated 8 months ago by
Jeremy
▴ 910 • written 8 months ago by
jinyu
▴ 10
2
votes
10
replies
874
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 5 weeks ago by
Ram
43k • written 10 weeks ago by
Sky
▴ 10
5
votes
10
replies
860
views
Error when viewing a bam file
samtools
updated 10 months ago by
Ram
43k • written 12 months ago by
Chris
▴ 260
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 17 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
14
votes
10
replies
954
views
How to remove center population from seurat cluster
single-cell
4 months ago by
synat.keam
▴ 100
5
votes
10
replies
1.3k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
8 months ago by
alwayshope
▴ 40
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 17 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
2
votes
10
replies
3.2k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 7 months ago by
Raygozak
★ 1.4k • written 5.8 years ago by
kakukeshi
▴ 80
1
vote
10
replies
3.1k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Kumar
▴ 120
1
vote
10
replies
1.7k
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 7 months ago by
jeffhsu3
• 0 • written 10 months ago by
fra.r.silvestro
▴ 10
8
votes
10
replies
758
views
bash script
whole-genome-sequencing
updated 19 days ago by
Ram
43k • written 26 days ago by
bestone
▴ 30
2
votes
9
replies
895
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 10 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
5 days ago by
anna
▴ 20
0
votes
9
replies
1.5k
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 7 months ago by
rfran010
▴ 900 • written 7 months ago by
pb11
▴ 10
1
vote
9
replies
907
views
Command line or python RNA-seq read simulator
simulation
RNA-seq
5 months ago by
i.sudbery
19k
4
votes
9
replies
596
views
variant calling
variant-calling
updated 4 weeks ago by
Ram
43k • written 4 weeks ago by
dalibenam64
• 0
0
votes
9
replies
933
views
fragments file generation via Sinto from CellRanger output
scATAC
alignment
scRNA
Sinto
10x
6 months ago by
ntsopoul
▴ 60
1
vote
9
replies
879
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 7 weeks ago by
Dave Carlson
★ 1.7k • written 7 weeks ago by
Matthew
• 0
0
votes
9
replies
551
views
Low number of both surviving reads after trimming
trimmomatic
trimming
5 weeks ago by
Jay
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 17 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
1,000 results • Page
2 of 20
Recent Votes
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
Answer: Design matrix Differential expression analysis
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Recent Replies
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 20
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 20
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
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by
Ruqaiya
• 0
This the tool still problematic?
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by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
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