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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
105
views
snpEff error. No CDS checked
snpEff
gtf
WES
4 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
104
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
4 days ago by
Maddie
• 0
1
vote
2
replies
196
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
3 days ago by
rheab1230
▴ 140
2
votes
4
replies
232
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 4 days ago by
Ram
39k • written 4 days ago by
miguellarrazlopezdenovales
• 0
0
votes
0
replies
82
views
Pore-C-Snakemake output files
contacts
4 days ago by
oksana03fel
• 0
1
vote
0
replies
105
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
4 days ago by
fr
▴ 200
0
votes
2
replies
171
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 4 days ago by
rpolicastro
12k • written 4 days ago by
Pac314
▴ 10
0
votes
2
replies
159
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
3 days ago by
survive
• 0
1
vote
1
reply
125
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 4 days ago by
GenoMax
129k • written 4 days ago by
hashim.rana11
▴ 20
2
votes
2
replies
156
views
Create customized gene annotation file
reference-genome
cellranger
12 hours ago by
rhonddaskl
• 0
0
votes
0
replies
78
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
4 days ago by
aziznasr1920
▴ 10
1
vote
3
replies
177
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 3 days ago by
Pierre Lindenbaum
154k • written 4 days ago by
herh
• 0
0
votes
0
replies
73
views
1000G reference panel for LD clumping
LD
4 days ago by
en_keser
• 0
0
votes
0
replies
82
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
4 days ago by
saladi
▴ 30
0
votes
2
replies
608
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 5 days ago by
Ram
39k • written 13 months ago by
Meeran
• 0
0
votes
7
replies
560
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 4 days ago by
Vincent Laufer
★ 2.9k • written 8 days ago by
Camilo Andres
▴ 30
0
votes
3
replies
199
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 4 days ago by
andres.firrincieli
3.3k • written 5 days ago by
kamanovae
▴ 80
0
votes
1
reply
152
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 5 days ago by
GenoMax
129k • written 5 days ago by
fafad046
• 0
0
votes
3
replies
185
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
3 days ago by
Mohd
▴ 20
1
vote
2
replies
174
views
sorting BAM file
BAM
updated 4 days ago by
ATpoint
72k • written 5 days ago by
Mohammad Amin
• 0
0
votes
0
replies
84
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 5 days ago by
zx8754
11k • written 5 days ago by
sidrah.maryam
▴ 50
0
votes
1
reply
144
views
Seurat: How to get all genes name of a cell ?
seurat
updated 4 days ago by
jv
★ 1.2k • written 5 days ago by
Picasa
▴ 640
1
vote
0
replies
232
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 4 days ago by
Ram
39k • written 5 days ago by
Supernova
• 0
0
votes
0
replies
101
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 5 days ago by
Ram
39k • written 5 days ago by
Fred
• 0
0
votes
1
reply
146
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 5 days ago by
Ram
39k • written 5 days ago by
chengc2016zzu
• 0
0
votes
0
replies
82
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
5 days ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
200
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
4 days ago by
Pegasus
▴ 90
0
votes
0
replies
119
views
Merging multiple PLINK files
plink
merging
6 days ago by
Nejla
• 0
0
votes
0
replies
116
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 6 days ago by
GenoMax
129k • written 6 days ago by
keiko.asakura
• 0
0
votes
2
replies
221
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
4 days ago by
J.F.Jiang
▴ 900
0
votes
2
replies
200
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 6 days ago by
Ram
39k • written 6 days ago by
Joel Wallenius
▴ 130
1
vote
3
replies
702
views
Regular Expression for conversion
Linux
grep
updated 5 days ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
164
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 4 days ago by
Ram
39k • written 6 days ago by
barrypraveen
▴ 110
0
votes
2
replies
172
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
6 days ago by
pg45863
• 0
0
votes
1
reply
139
views
ABySS Process Killed
ABySS
genome
assembly
updated 6 days ago by
GenoMax
129k • written 6 days ago by
asarcillo
• 0
0
votes
0
replies
96
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
6 days ago by
narges.bioinf
• 0
0
votes
3
replies
223
views
Query qbout single cell sequencing
fastq
ScRNA
updated 5 days ago by
Ram
39k • written 6 days ago by
abbas.waseem.gcu
▴ 20
0
votes
1
reply
179
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 5 days ago by
fracarb8
▴ 950 • written 6 days ago by
Sun
• 0
0
votes
1
reply
177
views
Why coordinate sort is required in sambamba depths?
sorting
coordinate
sambamba
linux
samtools
updated 6 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
MobiusT
▴ 10
0
votes
4
replies
281
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
7 days ago by
Ahmad
▴ 10
0
votes
2
replies
248
views
Error in download library file in expression console software
expression
microarray
console
5 days ago by
Mohammad
• 0
0
votes
6
replies
340
views
Demultiplexing bam file
demultiplexing
bam_file
Iontorrent
6 days ago by
hasani.iut6
▴ 60
1
vote
2
replies
263
views
DEgs RNAseq
RNAseq
7 days ago by
Juan
• 0
0
votes
0
replies
173
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
4 days ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
241
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 7 days ago by
Fabio Marroni
★ 3.0k • written 8 days ago by
1362321710
• 0
1
vote
1
reply
229
views
DownsampleSam
picard
DownsampleSam
updated 8 days ago by
Pierre Lindenbaum
154k • written 8 days ago by
mathalfilip
• 0
0
votes
1
reply
237
views
Error while running Megahit
Megahit
updated 7 days ago by
Mensur Dlakic
★ 23k • written 8 days ago by
abhiramiabhirami9072
• 0
2
votes
5
replies
413
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
5 days ago by
DanielEB_fisk
• 0
0
votes
0
replies
196
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
9 days ago by
dima
• 0
1
vote
0
replies
258
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics
single-cell
RNA
DEG
9 days ago by
abbas89
▴ 10
1,000 results • Page
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Recent Votes
Answer: [Meta] Use of AI
Answer: h5ad cellxgene to R
Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
Answer: Rna-Seq Pipeline
Comment: Create customized gene annotation file
Answer: [Meta] Use of AI
Discard Alignment With Mismatches From A Bam File
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Answer: WGCNA Trait File Issues
by
Jennifer M
• 0
![enter image description here][1] [1]: /media/images/0cf4eaa7-9550-4bbb-b43e-208dc787
Comment: Pairwise Alignment
by
WouterDeCoster
47k
> for whole genome analysis What do you mean with that? You provide too little information for us to answer your question.
Comment: Getting species names and taxa id from assembly accession number
by
GenoMax
129k
There must be some temporary glitch. Following command works (via EntrezDirect): $ esearch -db assembly -query GCA_000001405.29 | esu…
Comment: h5ad cellxgene to R
by
abmmki
• 0
matrix=adata.X.toarray() feature_names = adata.var['feature_name'] pd.DataFrame(data=matrix, index=adata.obs_names, c…
Comment: h5ad cellxgene to R
by
abmmki
• 0
I am trying use the same data and same method. But when I read the csv expression matrix in R, it frozen. Could you share your final seurat…
Comment: h5ad cellxgene to R
by
abmmki
• 0
I am trying use the same data and same method. But when I read the csv expression matrix in R, it frozen. Could you share your final seurat…
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now
by
eimanpharmacist
▴ 20
I think the problem in bowtie2 installation. it was installed using this: `conda install -c bioconda bowtie2` I removed it then re-installe…
Comment: Where to get the molecular subtype information of STAD sample in TCGA
by
Hamid Ghaedi
2.9k
Give `TCGAbiolinks` package a try.
Comment: How to calculate TPM from featureCounts output
by
survive
• 0
hi, So i will need to download the raw .fastq file from SRA and run salmon/Kallisto, instead of using the featureCounts?
Answer: calculate p value and associated z score for snp-gene pair
by
LChart
2.6k
The simplest thing to do would be to 'force' matrixeQTL to output everything by setting `pvOutputThreshold` to 1; this should give you all …
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now
by
eimanpharmacist
▴ 20
It is completed but I can not find any bam files, as you see above, I should get a bowtie2.bam file as an output but I did not.
Comment: [Meta] Use of AI
by
GenoMax
129k
It will be up to the people posting the AI assisted/generated comments/answers to add a disclaimer/note line to their posts for now. A butt…
Comment: Is a human genome file with reference as NCBI37 the same as hg19?
by
Ram
39k
Don't cross-post, especially on weekends. It looks like you're in a hurry and you don't care about annoying multiple communities.
Comment: Come work with me! Bioinformatician - Boston MA
by
Joseph
• 0
I am in Boston and my current position Principal Scientist in IHC, in situ Hybridization. I use Bioinformatics but don't have a formal degr…
Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
by
GenoMax
129k
Follow your normal analysis protocol. It is possible that your own data could have looked like this. While it is desirable to have upwards …
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