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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 11 months ago by
Ram
43k • written 5.7 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 5.2 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 4 weeks ago by
Ram
43k • written 6.9 years ago by
lessismore
★ 1.3k
0
votes
8
replies
10.0k
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
7.9k
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
2
votes
9
replies
7.7k
views
6 follow
Read MAP and PED files in PLINK
GWAS
PLINK
updated 4 months ago by
GenoMax
142k • written 6.0 years ago by
ft821525
• 0
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 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
7
replies
7.3k
views
Problem in in alignment by muscle
sequence
muscle
alignment
updated 10 months ago by
Ram
43k • written 6.8 years ago by
misbahabas
▴ 70
6
votes
4
replies
6.6k
views
What is gnomAD allele frequency
AF
gnomAD
updated 4 months ago by
Lhl
▴ 760 • written 3.1 years ago by
Eric Wang
▴ 50
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 17 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
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 6.3 years ago by
win
▴ 980
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
6.2k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 4 weeks ago by
Ram
43k • written 5.6 years ago by
modarzi
▴ 170
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 4 weeks ago by
Ram
43k • written 7.7 years ago by
gokce.ouz
▴ 70
3
votes
14
replies
6.1k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn
mbedtls
blast
linux
blast+
updated 4 months ago by
K.Gee
▴ 40 • written 3.1 years ago by
janneken0210
• 0
2
votes
14
replies
6.0k
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
6.0k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 29 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 10 months ago by
Ram
43k • written 11.2 years ago by
stu.andrews
• 0
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 9 months ago by
ATpoint
82k • written 5.1 years ago by
Joel Wallenius
▴ 210
0
votes
1
reply
5.4k
views
Hapmap to vcf
vcf
hapmap
updated 10 months ago by
Ram
43k • written 5.7 years ago by
shinken123
▴ 150
0
votes
8
replies
5.4k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 5 weeks ago by
EricYang
• 0 • written 4.8 years ago by
Dan
▴ 180
2
votes
11
replies
5.3k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 4 months ago by
e.r.zakiev
▴ 210 • 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 11 months ago by
Ram
43k • written 4.3 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
10 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 4.5 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 7.8 years ago by
BCArg
▴ 90
1
vote
9
replies
4.6k
views
Unable to install bioconda and bowtie
bioconda
conda
updated 5 months ago by
rpolicastro
13k • written 20 months ago by
n.anuragsharma
▴ 40
7
votes
13
replies
4.5k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq
trimming
fastqc
updated 6 months ago by
ATpoint
82k • written 3.5 years ago by
Pac314
▴ 10
0
votes
8
replies
4.5k
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
4.5k
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 5 months ago by
Ram
43k • written 6.0 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 10 months ago by
Ram
43k • written 7.9 years ago by
Ghoul
▴ 10
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
4.3k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 5 weeks ago by
Ram
43k • written 5.1 years ago by
RNAseqer
▴ 270
7
votes
8
replies
4.3k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 11 months ago by
Ram
43k • written 4.0 years ago by
kand3e
▴ 60
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 4 weeks ago by
Ram
43k • written 7.7 years ago by
Lluís R.
★ 1.2k
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 5 weeks 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
88k • written 5.5 years ago by
divya.nandakumar
▴ 30
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
2
votes
4
replies
4.0k
views
Transcriptomic Coordinate Bam To Genomic Coordinate Bam
bam
genomics
updated 10 months ago by
Ram
43k • written 11.3 years ago by
Ge
▴ 80
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
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 5 months ago by
jv
★ 1.8k • written 2.4 years ago by
yang.zhizhang
▴ 10
0
votes
16
replies
3.9k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 12 months ago by
Ram
43k • written 6.0 years ago by
rororo
▴ 10
0
votes
7
replies
3.8k
views
MUMmer plot visualization
MUMmer plot
updated 3 months ago by
Carlos
• 0 • written 3.3 years ago by
rthapa
▴ 90
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 13 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
1,000 results • Page
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Recent Votes
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
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Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
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ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
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