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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 10 months ago by
Ram
43k • written 5.6 years ago by
Shahzad
▴ 30
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Star
▴ 60
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 12 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
0
votes
8
replies
9.9k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.8 years ago by
himanimalhotra89
• 0
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 8 months ago by
Ram
43k • written 8.0 years ago by
nikelle.petrillo
▴ 110
4
votes
12
replies
7.8k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 11 weeks ago by
mgdrnl
▴ 10 • written 3.4 years ago by
whb
▴ 60
2
votes
9
replies
7.6k
views
6 follow
Read MAP and PED files in PLINK
GWAS
PLINK
updated 4 months ago by
GenoMax
141k • written 6.0 years ago by
ft821525
• 0
0
votes
7
replies
7.2k
views
Problem in in alignment by muscle
sequence
muscle
alignment
updated 10 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 18 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
6
votes
4
replies
6.5k
views
What is gnomAD allele frequency
AF
gnomAD
updated 3 months ago by
Lhl
▴ 760 • written 3.1 years ago by
Eric Wang
▴ 50
3
votes
7
replies
6.4k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 11 months ago by
DareDevil
★ 4.3k • written 6.2 years ago by
win
▴ 970
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly
Trinity
RNA-seq
trimmomatic
updated 10 months ago by
Ram
43k • written 8.1 years ago by
lay_0
▴ 50
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 12 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 12 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
3
votes
14
replies
5.9k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn
mbedtls
blast
linux
blast+
updated 3 months ago by
K.Gee
▴ 40 • written 3.1 years ago by
janneken0210
• 0
2
votes
14
replies
5.9k
views
Using sam-dump in SRA toolkit to download chr20.bam from NA12878
sratoolkit
sam-dump
updated 10 months ago by
Ram
43k • written 7.1 years ago by
Covux
▴ 10
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 9 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
4
replies
5.9k
views
using IGV to visualize RNA seq alignment to transcriptome
rna-seq
igv
alignment
updated 8 months ago by
Ram
43k • written 7.9 years ago by
nikelle.petrillo
▴ 110
1
vote
5
replies
5.8k
views
Generate VCF File from Bam file and fasta by GATK
vcf
SNP
genome
next-gen
updated 10 months ago by
Ram
43k • written 6.8 years ago by
misbahabas
▴ 70
0
votes
3
replies
5.6k
views
Bedgraphtobigwig Conversion Difficulties
bigwig
updated 9 months ago by
Ram
43k • written 11.2 years ago by
stu.andrews
• 0
1
vote
4
replies
5.5k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R
heatmap
updated 11 months ago by
Ram
43k • written 6.2 years ago by
chetana
▴ 60
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq
rna-seq
htseq
FPKM
TPM
updated 8 months ago by
ATpoint
82k • written 5.0 years ago by
Joel Wallenius
▴ 210
0
votes
1
reply
5.3k
views
Hapmap to vcf
vcf
hapmap
updated 9 months ago by
Ram
43k • written 5.6 years ago by
shinken123
▴ 150
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 19 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
4
replies
5.3k
views
Sequence alignment length
multiple-sequence-alignment
updated 11 months ago by
Ram
43k • written 7.2 years ago by
biobudhan
▴ 20
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
▴ 200 • written 7.8 years ago by
CAnna
▴ 20
3
votes
4
replies
5.2k
views
What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
RNA-Seq
updated 9 months ago by
tirza.doniger
▴ 10 • written 8.7 years ago by
tiago211287
★ 1.4k
10
votes
14
replies
5.0k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 10 months ago by
Ram
43k • written 4.2 years ago by
gable_works
▴ 50
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.3 years ago by
stu111538
▴ 80
1
vote
4
replies
4.8k
views
TCGA data(RPKM) differential gene expression
rna-seq
R
TCGA
RPKM
IPA
9 months ago by
realnewbie
▴ 30
3
votes
2
replies
4.8k
views
How to plot a circular clustered heatmap with dendrogram
circular heatmap
updated 9 months ago by
logbio
▴ 30 • written 4.4 years ago by
The
▴ 180
2
votes
7
replies
4.7k
views
SRA toolkit internet settings
sratoolkit
fastq-dump
sequencing
RNA-Seq
updated 10 months ago by
Ram
43k • written 7.7 years ago by
BCArg
▴ 90
0
votes
8
replies
4.4k
views
Downloading single cell data from NCBI
ncbi
rna-seq
fastq-dump
single-cell
updated 8 months ago by
Ram
43k • written 5.4 years ago by
V
▴ 380
0
votes
7
replies
4.4k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq
alignment
software-error
next-gen
sequence
updated 4 months ago by
Ram
43k • written 5.9 years ago by
nasreenbano91
• 0
1
vote
0
replies
4.4k
views
how to convert .geno/.snp/.ind to .bed/.bim/.fam (ped plink format) in Windows
plink
genomes
ancestrymap
updated 9 months ago by
Ram
43k • written 7.9 years ago by
Ghoul
▴ 10
7
votes
13
replies
4.4k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq
trimming
fastqc
updated 5 months ago by
ATpoint
82k • written 3.4 years ago by
Pac314
▴ 10
1
vote
9
replies
4.4k
views
Unable to install bioconda and bowtie
bioconda
conda
updated 4 months ago by
rpolicastro
13k • written 19 months ago by
n.anuragsharma
▴ 30
3
votes
4
replies
4.4k
views
Atypical volcano plot RNA-seq
volcano-plot
RNA-seq
deseq2
updated 8 months ago by
Ram
43k • written 5.5 years ago by
Teresa
▴ 20
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 19 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 10 months ago by
Ram
43k • written 3.9 years ago by
kand3e
▴ 60
3
votes
4
replies
4.1k
views
What are the Pros and Cons of working in Bioinformatics???
career
bio
updated 11 months ago by
Ram
43k • written 6.2 years ago by
scottschu97
▴ 20
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 10 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
0
votes
4
replies
4.1k
views
What is Dunn's multiple comparison test?
statistics
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Koreanraichu
• 0
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 19 days ago by
Ram
43k • written 5.6 years ago by
lkianmehr
▴ 100
1
vote
7
replies
4.1k
views
Adjust width of annotations in pheatmap
R
heatmap
updated 7 months ago by
Kevin Blighe
87k • written 5.5 years ago by
divya.nandakumar
▴ 30
2
votes
4
replies
4.0k
views
Transcriptomic Coordinate Bam To Genomic Coordinate Bam
bam
genomics
updated 9 months ago by
Ram
43k • written 11.3 years ago by
Ge
▴ 80
5
votes
19
replies
4.0k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 4 months ago by
ATpoint
82k • written 4.9 years ago by
ta_awwad
▴ 340
1
vote
5
replies
4.0k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 11 months ago by
Ram
43k • written 7.7 years ago by
Biogeek
▴ 470
1
vote
8
replies
3.9k
views
No gene can be mapped
R
GSEA
updated 4 months ago by
jv
★ 1.8k • written 2.3 years ago by
yang.zhizhang
• 0
0
votes
5
replies
3.9k
views
Phylogeny Heatmap with Python
multiple-sequence-alignment
updated 11 months ago by
Ram
43k • written 5.1 years ago by
marina.gerges
• 0
1,000 results • Page
1 of 20
Recent Votes
Answer: High Malat-1 expression in single cell data
Answer: High Malat-1 expression in single cell data
The Biostar Herald for Monday, April 29, 2024
A: Bam And Indexed Bam Files
High Malat-1 expression in single cell data
Segmentation fault using gemma
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Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
Malat1 is a lncRNA abundant in the nucleus. I guess if Malat1 is abundant and stable, makes sense it could be detect in high amounts in scR…
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Where can I ask this question? Apparently this the place where you can help for toil?
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Dear Gordon, excuse me for not being specific regarding your advice. What would be the best way if I wanted to add new annotations to the …
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While you wait to get answers, consider asking ChatGPT for a solution. You may be pleasantly surprised with pointers/code you will get.
Comment: High Malat-1 expression in single cell data
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When I perform differential analysis, the genes that could be considered as markers in this malat1 high cluster tend to be nuclear genes. D…
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You can check where the application was installed using: https://unix.stackexchange.com/questions/39590/apt-get-install-where-does-it-go T…
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"using RNA-seq for allele imbalanced gene expression" -> Not sure what you mean by that; thousands of studies (including some ongoing studi…
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by
Kazo
▴ 10
I have noticed in articles that people define low-quality clusters and remove them from the data, but they don't exactly explain what makes…
Answer: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
I'm assuming you read https://kb.10xgenomics.com/hc/en-us/articles/360004729092-Why-do-I-see-high-levels-of-Malat1-in-my-gene-expression-da…
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I actually advised you not to remove duplicate probes, especially as you seem to be use probe annotation that is very old and possibly out …
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Hello, were you able to rectify this. If yes, do tell. I am getting a similar error. Thank you
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If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes …
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Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
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You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
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