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1,000 results • Page 5 of 20
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0
votes
0
replies
195
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
20 days ago by simplitia ▴ 130
1
vote
1
reply
264
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 20 days ago by 82k • written 20 days ago by • 0
0
votes
0
replies
181
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary deeptools correlation
2 days ago by Emily ▴ 20
1
vote
0
replies
192
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
20 days ago by rohitsatyam102 ▴ 860
0
votes
0
replies
174
views
how to read graph_test output of monocle 3
monocle3
20 days ago by synat.keam ▴ 100
0
votes
1
reply
533
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 21 days ago by • 0 • written 5 months ago by • 0
0
votes
0
replies
175
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
21 days ago by Aspire ▴ 330
0
votes
4
replies
413
views
Highest variable features in single cell data
single-cell
9 days ago by carolofharvest ▴ 40
1
vote
3
replies
448
views
PCA plot
DESeq2 PCAplot
updated 17 days ago by 4.2k • written 21 days ago by ▴ 10
0
votes
0
replies
171
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
21 days ago by 4fzcgueyp5 • 0
0
votes
2
replies
311
views
Annovar using R package
Annovar gnomAD R
20 days ago by DKA ▴ 40
0
votes
5
replies
438
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 21 days ago by 142k • written 22 days ago by ▴ 90
0
votes
0
replies
167
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 21 days ago by 43k • written 22 days ago by • 0
0
votes
0
replies
329
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
22 days ago by pramach1 ▴ 40
0
votes
1
reply
206
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 21 days ago by • 0 • written 22 days ago by • 0
0
votes
0
replies
167
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
22 days ago by salias • 0
0
votes
5
replies
457
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 19 days ago by 100k • written 22 days ago by ▴ 10
0
votes
0
replies
141
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 21 days ago by 43k • written 22 days ago by • 0
1
vote
2
replies
280
views
alignment result
RNA-seq samtools hisat2
21 days ago by ahmad.sajad4541 • 0
0
votes
0
replies
140
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
22 days ago by Kash ▴ 110
0
votes
1
reply
189
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 22 days ago by ★ 27k • written 22 days ago by • 0
2
votes
2
replies
334
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 21 days ago by 43k • written 22 days ago by ▴ 140
2
votes
9
replies
936
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 22 days ago by 4.2k • written 7 months ago by • 0
0
votes
11
replies
709
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
20 days ago by atowns21 • 0
0
votes
1
reply
212
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 22 days ago by ★ 2.4k • written 22 days ago by • 0
0
votes
0
replies
120
views
The concept of co-occurrence network structure
co-occurence microbiome network
22 days ago by ohtang7 ▴ 40
0
votes
1
reply
207
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 23 days ago by 142k • written 23 days ago by ▴ 20
0
votes
5
replies
426
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
22 days ago by njornet ▴ 20
0
votes
0
replies
125
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
0
replies
128
views
Merging replicates from Encode project
CHIP-seq encode
23 days ago by Nurken • 0
1
vote
3
replies
299
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
23 days ago by WouterDeCoster 47k
1
vote
3
replies
334
views
some error in building kraken2 database
metagenome kraken2
22 days ago by Art1ess • 0
0
votes
1
reply
212
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 22 days ago by ★ 2.4k • written 23 days ago by ▴ 110
1
vote
1
reply
212
views
Failed kmer content
kmer illumina ngs
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
0
replies
115
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 22 days ago by 43k • written 23 days ago by • 0
0
votes
1
reply
175
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
8
replies
454
views
Error in cnetplot enrichplot package
R
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
0
replies
128
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 23 days ago by 43k • written 23 days ago by ▴ 200
0
votes
0
replies
113
views
Analysis of the gene family of a genome.
Genome gene-family
updated 23 days ago by 43k • written 23 days ago by ▴ 90
0
votes
0
replies
116
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
0
replies
222
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 23 days ago by 43k • written 23 days ago by ▴ 20
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 23 days ago by 10k • written 6.2 years ago by ▴ 10
1
vote
8
replies
532
views
Downsampling fastq file
downsample fastq
15 days ago by marco.barr ▴ 120
0
votes
1
reply
168
views
tbtool
tbtool
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
10
replies
610
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 16 days ago by 19k • written 24 days ago by • 0
0
votes
1
reply
161
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 24 days ago by 82k • written 24 days ago by • 0
0
votes
0
replies
105
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
24 days ago by manaswwm ▴ 510
0
votes
0
replies
96
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
23 days ago by alifafiq1 • 0
0
votes
0
replies
102
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
24 days ago by feather-W • 0
2
votes
4
replies
376
views
interpretartion of a vcf file
calling genotype ONT variant diploid
22 days ago by samuelkalandarov2002 ▴ 10
1,000 results • Page 5 of 20
Recent Votes
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: getting exon coordinates
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
Answer: Concatenate multiple paired-end reads or interleaved which is best approach to a
Scale total height phylogenetic tree
Scale total height phylogenetic tree
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
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Scholar to GenoMax 142k
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Recent Replies
Answer: mitochondrial genome assembly pipeline by shelkmike ★ 1.2k
A good tool for mitochondrial genome assembly is GetOrganelle (https://github.com/Kinggerm/GetOrganelle)
Comment: getting exon coordinates by Ram 43k
Please do not use `bioinformatics` as a tag unless your post in about the field of bioinformatics itself.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Ram 43k
I've removed unneccessary tags - `meta` and `how-to` don't apply to this post at all, and the `forum` tag is not in use anymore.
Comment: Difference in number of reads when using duplex and simplex base calling with Do by GenoMax 142k
I assume you have posted this in nanopore community and/or on the dorado issues page on GitHub. Please come back and post an update once yo…
Comment: Annotating file using bcftools by kl ▴ 10
Do you know if there is a way to leave chr:pos in ID if there is no matching rsid based on chromosome and position, as variants have been r…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver by Jeremy Leipzig 22k
We get this question like clockwork every 6 weeks. I'll say it one more time: **A freeze is a freeze.** Patches are not a thing th…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline? by ev97 ▴ 20
Thanks very much for your feedback! I will take all those things in consideration once I start the analysis! Just out of curiosity, do yo…
Answer: getting exon coordinates by ben@f ▴ 10
A combination of bash and awk can do the work, suppose you have the gff file annotation of your gene of interest and a text file with Gene…
Comment: getting exon coordinates by Pierre Lindenbaum 161k
https://www.biostars.org/p/385786/ ; <br> https://www.biostars.org/p/276608/ ; <br> https://www.biostars.org/p/411934/ ;etc... <!-- How …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by GenoMax 142k
I would have thought `needle` from EMBOSS would be the option to use.
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 120
ok, then you should add the donor information to the PCA analysis. First create a separate dataframe for the donors, then add with `factor`…
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences? by b.contreras.moreira ▴ 180
If you are willing to do some coding I think <https://github.com/smarco/WFA2-lib> is among the fastest global aligners, the repo has C++ ex…
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame by GenoMax 142k
There is an API that you could try: https://www.ebi.ac.uk/pride/markdownpage/prideutilities
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame by Pierre Lindenbaum 161k
thanks. looks interesting but it's broken. the Firefox console shows a 404 for https://www.ebi.ac.uk/pride/ws/archive/v2/peptidesummary?ke…
Answer: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame by GenoMax 142k
Perhaps: https://www.ebi.ac.uk/pride/peptidome/ This site is very slow. Almost to the point of being not usable. My search with your pepti…
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