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0
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52
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Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes vcf phasing
4 hours ago by HarperReed • 0
0
votes
2
replies
67
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genome assembly records not present in assembly_summary.txt
ncbi bacteria assembly
updated 1 hour ago by 141k • written 4 hours ago by ▴ 10
1
vote
0
replies
43
views
Simulation of label-free bottom-up proteomics expression dataset
label-free bottom-up lc-ms proteomics
6 hours ago by KABILAN ▴ 50
0
votes
0
replies
44
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Running Phylogenetic Analysis With NCBI Genome
population genetics phylogenetic species sequencing
6 hours ago by SineWave • 0
0
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0
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42
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RNA-seq: full length gene
identification gene full length
7 hours ago by Nargis • 0
0
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3
replies
167
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Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 5 hours ago by 161k • written 8 hours ago by • 0
0
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0
replies
38
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly phased Haplotype Annotation
9 hours ago by turcoa1 • 0
0
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0
replies
59
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Designing single-stable RNA molecules
structure RNA
15 hours ago by Edna • 0
0
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0
replies
68
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
15 hours ago by simplitia ▴ 130
0
votes
1
reply
106
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 16 hours ago by 82k • written 17 hours ago by • 0
0
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0
replies
72
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
19 hours ago by avocado123 • 0
0
votes
0
replies
63
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary correlation
20 hours ago by Emily ▴ 10
1
vote
0
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80
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
20 hours ago by rohitsatyam102 ▴ 850
0
votes
0
replies
65
views
how to read graph_test output of monocle 3
monocle3
21 hours ago by synat.keam ▴ 100
0
votes
1
reply
397
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 22 hours ago by • 0 • written 4 months ago by • 0
0
votes
0
replies
82
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
1 day ago by Aspire ▴ 300
0
votes
2
replies
162
views
Highest variable features in single cell data
single-cell
updated 16 hours ago by 43k • written 1 day ago by • 0
0
votes
2
replies
187
views
PCA plot
DESeq2 PCAplot
updated 3 hours ago by 82k • written 1 day ago by ▴ 10
0
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0
replies
105
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
1 day ago by 4fzcgueyp5 • 0
0
votes
2
replies
209
views
Annovar using R package
Annovar gnomAD R
16 hours ago by DKA ▴ 40
0
votes
5
replies
287
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 23 hours ago by 141k • written 1 day ago by ▴ 90
0
votes
0
replies
129
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
0
replies
247
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
1 day ago by pramach1 ▴ 40
0
votes
1
reply
139
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 1 day ago by • 0 • written 2 days ago by • 0
0
votes
0
replies
130
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
2 days ago by salias • 0
0
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4
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250
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
1 day ago by sehriban.buyukkilic ▴ 10
0
votes
0
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112
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 1 day ago by 43k • written 2 days ago by • 0
1
vote
2
replies
197
views
alignment result
RNA-seq samtools hisat2
1 day ago by ahmad.sajad4541 • 0
0
votes
0
replies
94
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet DoubletFinder Seurat modelHomotypic
updated 1 day ago by 43k • written 2 days ago by • 0
0
votes
0
replies
104
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
2 days ago by Kash ▴ 110
0
votes
1
reply
144
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 2 days ago by ★ 27k • written 2 days ago by • 0
0
votes
2
replies
236
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 1 day ago by 43k • written 2 days ago by ▴ 140
2
votes
9
replies
820
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 2 days ago by 4.2k • written 6 months ago by • 0
0
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11
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467
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
13 hours ago by atowns21 • 0
0
votes
1
reply
150
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 2 days ago by ★ 2.4k • written 2 days ago by • 0
0
votes
0
replies
93
views
The concept of co-occurrence network structure
co-occurence microbiome network
2 days ago by ohtang7 ▴ 40
0
votes
1
reply
153
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 2 days ago by 141k • written 3 days ago by ▴ 20
0
votes
5
replies
286
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
2 days ago by njornet ▴ 20
0
votes
0
replies
87
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
95
views
Merging replicates from Encode project
CHIP-seq encode
3 days ago by Nurken • 0
1
vote
3
replies
205
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
3 days ago by WouterDeCoster 47k
1
vote
3
replies
248
views
some error in building kraken2 database
metagenome kraken2
2 days ago by Art1ess • 0
0
votes
1
reply
129
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 2 days ago by ★ 2.4k • written 3 days ago by ▴ 110
1
vote
1
reply
166
views
Failed kmer content
kmer illumina ngs
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
86
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
1
reply
143
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
8
replies
307
views
Error in cnetplot enrichplot package
R
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
107
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 3 days ago by 43k • written 3 days ago by ▴ 200
0
votes
0
replies
92
views
Analysis of the gene family of a genome.
Genome gene-family
updated 3 days ago by 43k • written 3 days ago by ▴ 80
0
votes
0
replies
94
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 2 days ago by 43k • written 3 days ago by • 0
1,000 results • Page 1 of 20
Recent Votes
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
Converting between Ensembl Versions
Comment: what is the purpose of indexing the reference genome (Kallisto)
Answer: what is the purpose of indexing the reference genome (Kallisto)
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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Supporter to Jalil Sharif ▴ 80
Popular Question to sil_bioinfo ▴ 40
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Recent Replies
Comment: ScRNA data question by starswillfade ▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question by starswillfade ▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt by GenoMax 141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto) by i.sudbery 19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by benformatics 3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto) by dsull ★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by Jalil Sharif ▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis by The_PyPanda ▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads by Antonio R. Franco ★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
Comment: PCA plot by ATpoint 82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
Comment: genome assembly records not present in assembly_summary.txt by Joe 21k
If you have the accession numbers can you not use something like `eutils`?
Comment: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files by J • 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
> using bcftools Show us what you tried
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