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1,000 results • Page 3 of 20
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0
votes
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152
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Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
9 days ago by 4fzcgueyp5 • 0
0
votes
2
replies
267
views
Annovar using R package
Annovar gnomAD R
8 days ago by DKA ▴ 40
0
votes
5
replies
374
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 8 days ago by 142k • written 9 days ago by ▴ 90
0
votes
0
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148
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 9 days ago by 43k • written 9 days ago by • 0
0
votes
0
replies
311
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
9 days ago by pramach1 ▴ 40
0
votes
1
reply
176
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 9 days ago by • 0 • written 9 days ago by • 0
0
votes
0
replies
149
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
10 days ago by salias • 0
0
votes
5
replies
370
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 6 days ago by 100k • written 10 days ago by ▴ 10
0
votes
0
replies
128
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 9 days ago by 43k • written 10 days ago by • 0
1
vote
2
replies
249
views
alignment result
RNA-seq samtools hisat2
9 days ago by ahmad.sajad4541 • 0
0
votes
0
replies
119
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
10 days ago by Kash ▴ 110
0
votes
1
reply
168
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 10 days ago by ★ 27k • written 10 days ago by • 0
2
votes
2
replies
301
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 9 days ago by 43k • written 10 days ago by ▴ 140
2
votes
9
replies
887
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 10 days ago by 4.2k • written 6 months ago by • 0
0
votes
11
replies
616
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
8 days ago by atowns21 • 0
0
votes
1
reply
184
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 10 days ago by ★ 2.4k • written 10 days ago by • 0
0
votes
0
replies
107
views
The concept of co-occurrence network structure
co-occurence microbiome network
10 days ago by ohtang7 ▴ 40
0
votes
1
reply
185
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 10 days ago by 142k • written 10 days ago by ▴ 20
0
votes
5
replies
373
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
9 days ago by njornet ▴ 20
0
votes
0
replies
103
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 10 days ago by 43k • written 10 days ago by • 0
0
votes
0
replies
112
views
Merging replicates from Encode project
CHIP-seq encode
10 days ago by Nurken • 0
1
vote
3
replies
264
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
10 days ago by WouterDeCoster 47k
1
vote
3
replies
302
views
some error in building kraken2 database
metagenome kraken2
10 days ago by Art1ess • 0
0
votes
1
reply
181
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 10 days ago by ★ 2.4k • written 11 days ago by ▴ 110
1
vote
1
reply
195
views
Failed kmer content
kmer illumina ngs
updated 10 days ago by 43k • written 11 days ago by • 0
0
votes
0
replies
99
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 10 days ago by 43k • written 11 days ago by • 0
0
votes
1
reply
159
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 11 days ago by 43k • written 11 days ago by • 0
0
votes
8
replies
391
views
Error in cnetplot enrichplot package
R
updated 11 days ago by 43k • written 11 days ago by • 0
0
votes
0
replies
117
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 11 days ago by 43k • written 11 days ago by ▴ 200
0
votes
0
replies
103
views
Analysis of the gene family of a genome.
Genome gene-family
updated 11 days ago by 43k • written 11 days ago by ▴ 80
0
votes
0
replies
107
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 10 days ago by 43k • written 11 days ago by • 0
0
votes
0
replies
212
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 11 days ago by 43k • written 11 days ago by ▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 11 days ago by 10k • written 6.2 years ago by ▴ 10
1
vote
8
replies
466
views
Downsampling fastq file
downsample fastq
3 days ago by marco.barr ▴ 90
0
votes
1
reply
149
views
tbtool
tbtool
updated 11 days ago by 43k • written 11 days ago by • 0
0
votes
10
replies
507
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 4 days ago by 19k • written 11 days ago by • 0
0
votes
1
reply
141
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 11 days ago by 82k • written 11 days ago by • 0
0
votes
0
replies
97
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
11 days ago by manaswwm ▴ 510
0
votes
0
replies
85
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
10 days ago by alifafiq1 • 0
0
votes
0
replies
92
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
11 days ago by feather-W • 0
2
votes
4
replies
330
views
interpretartion of a vcf file
calling genotype ONT variant diploid
10 days ago by samuelkalandarov2002 ▴ 10
0
votes
0
replies
92
views
Annotating single cell data automatically
cell annotation single
11 days ago by Gerard • 0
0
votes
1
reply
176
views
RNA-seq bacteria contamination
RNA-seq
updated 11 days ago by 142k • written 12 days ago by • 0
0
votes
0
replies
83
views
Imputation advice
imputation
12 days ago by kl ▴ 10
0
votes
0
replies
104
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
12 days ago by Enrique • 0
0
votes
0
replies
83
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
12 days ago by sativus ▴ 20
0
votes
0
replies
90
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
12 days ago by Biostars2200 • 0
0
votes
0
replies
142
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 12 days ago by 8.7k • written 12 days ago by • 0
2
votes
5
replies
493
views
Marking duplicates using UMIs
Deduplication UMI
updated 12 days ago by 19k • written 13 days ago by • 0
0
votes
0
replies
147
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 12 days ago by 43k • written 13 days ago by • 0
1,000 results • Page 3 of 20
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Answer: RNA velocity for smart-seq2 dataset
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A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
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Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA by Thanujay S • 0
Hey! Can you explain the question further? What have you tried?
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I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
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> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
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Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
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You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
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The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon. by lcordeiro ▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome by chrchang523 10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file? by chrchang523 10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA by bk11 ★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
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Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
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![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
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In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
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