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128 results • Page 1 of 3
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare how-to
32 minutes ago by glaciya2018 • 0
0
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0
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16
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roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
55 minutes ago by pramach1 ▴ 40
0
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0
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30
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GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
3 hours ago by mawigoj318 • 0
0
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0
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54
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Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
5 hours ago by salias • 0
0
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2
replies
87
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different FeatureCounts output for the same data
fpkm rnaseq Counts Rsubread
updated 2 hours ago by 100k • written 5 hours ago by ▴ 10
0
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0
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43
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Alternative splicing analysis using SUPPA tool - how to normalise counts?
single-cell suppa rnaseq splicing alternative
10 minutes ago by newuser2024 • 0
0
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0
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37
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Network Alignment
plugin Cytoscape CytoMCS
6 hours ago by Akash D ▴ 40
0
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1
reply
70
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alignment result
RNA-seq samtool analysis hisat2
updated 3 hours ago by 141k • written 7 hours ago by • 0
0
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0
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43
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Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet hetero Seurat modelHomotypic DoubletFinder
8 hours ago by Jeyong • 0
0
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1
reply
73
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PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 22 minutes ago by ▴ 170 • written 10 hours ago by • 0
0
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0
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58
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
15 hours ago by Kash ▴ 110
0
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1
reply
95
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How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 11 hours ago by ★ 27k • written 17 hours ago by • 0
0
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2
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173
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage FASTA alignment identity
updated 6 hours ago by ▴ 170 • written 17 hours ago by ▴ 140
2
votes
9
replies
767
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TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 13 hours ago by 4.2k • written 6 months ago by • 0
0
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10
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333
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How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
11 hours ago by atowns21 • 0
0
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1
reply
109
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Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 19 hours ago by ★ 2.3k • written 20 hours ago by • 0
0
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0
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68
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The concept of co-occurrence network structure
co-occurence microbiome network
23 hours ago by ohtang7 ▴ 40
0
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1
reply
122
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Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 1 day ago by 141k • written 1 day ago by ▴ 20
0
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5
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239
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
3 hours ago by njornet ▴ 20
0
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0
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70
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 23 hours ago by 43k • written 1 day ago by • 0
0
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0
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82
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Merging replicates from Encode project
CHIP-seq encode
1 day ago by Nurken • 0
1
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3
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181
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Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
1 day ago by WouterDeCoster 47k
1
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3
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219
views
some error in building kraken2 database
metagenome kraken2
13 hours ago by Art1ess • 0
0
votes
1
reply
114
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Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 23 hours ago by ★ 2.3k • written 1 day ago by ▴ 110
1
vote
1
reply
147
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Failed kmer content
kmer illumina ngs
updated 23 hours ago by 43k • written 1 day ago by • 0
0
votes
1
reply
181
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Heatmap and rna-seq
RNA-Seq Heatmap and
updated 16 hours ago by 100k • written 1 day ago by ▴ 10
0
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0
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76
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 23 hours ago by 43k • written 1 day ago by • 0
0
votes
1
reply
129
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 1 day ago by 43k • written 1 day ago by • 0
0
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8
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266
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Error in cnetplot enrichplot package
R
updated 1 day ago by 43k • written 1 day ago by • 0
0
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0
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101
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Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 1 day ago by 43k • written 1 day ago by ▴ 200
0
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0
replies
84
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Analysis of the gene family of a genome.
Genome gene-family
updated 1 day ago by 43k • written 1 day ago by ▴ 80
0
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0
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89
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File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 23 hours ago by 43k • written 1 day ago by • 0
0
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0
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131
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Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 1 day ago by 43k • written 1 day ago by ▴ 10
1
vote
3
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2.4k
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Problem to remove subset of patients with plink
plink PED
updated 1 day ago by 10k • written 6.1 years ago by ▴ 10
1
vote
5
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231
views
Downsampling fastq file
downsample fastq
updated 1 day ago by 43k • written 1 day ago by ▴ 80
0
votes
1
reply
118
views
tbtool
tbtool
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
2
replies
172
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Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 1 day ago by 19k • written 2 days ago by • 0
0
votes
2
replies
140
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 1 day ago by ★ 27k • written 2 days ago by ▴ 120
0
votes
1
reply
112
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 2 days ago by 82k • written 2 days ago by • 0
0
votes
0
replies
78
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
2 days ago by manaswwm ▴ 490
0
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0
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68
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
1 day ago by alifafiq1 • 0
0
votes
0
replies
77
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
2 days ago by feather-W • 0
2
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4
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226
views
interpretartion of a vcf file
calling genotype ONT variant diploid
6 hours ago by samuelkalandarov2002 ▴ 10
0
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0
replies
74
views
Annotating single cell data automatically
cell annotation single
2 days ago by Gerard • 0
0
votes
1
reply
136
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by 141k • written 2 days ago by • 0
0
votes
0
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66
views
Imputation advice
imputation
2 days ago by kl ▴ 10
0
votes
0
replies
81
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
2 days ago by Enrique • 0
0
votes
0
replies
68
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
2 days ago by sativus ▴ 20
0
votes
0
replies
74
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
2 days ago by Biostars2200 • 0
0
votes
0
replies
115
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 2 days ago by 8.7k • written 2 days ago by • 0
128 results • Page 1 of 3
Recent Votes
What are Tiles in Sequencing
What are Tiles in Sequencing
Answer: How to trim transcripts using information from NCBI contamination screen report
Difference Between "Mate Pair" And "Pair-End"
Difference Between "Mate Pair" And "Pair-End"
Comment: To get p-values for the TPM
Comment: HaplotypeCaller - only SNPs
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Recent Replies
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by Bertalan_Takacs ▴ 90
Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
Answer: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Hey, can you please show me a few lines of your phenotype updated .fam file? I m seeing there are 7 columns in it, that might me the proble…
Comment: PCA plot (Suggestions Needed) by jkim ▴ 170
How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype differenc…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data by Istvan Albert 100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by mropri ▴ 150
Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
I think the blog post lines up wit both of our statements. It seems that 2-way binning (pass/fail) already dramatically improves the calls…
Comment: Tax4Fun2 - error by drstalinantony28 • 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Windo…
Answer: Tax4Fun2 - error by drstalinantony28 • 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Win…
Comment: different FeatureCounts output for the same data by GenoMax 141k
> featureCounts alignment rate is only around 15-20%. You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result by GenoMax 141k
> 20386810 (88.67%) aligned concordantly exactly 1 time This result is fine.
Comment: To get p-values for the TPM by ATpoint 82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment? by njornet ▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
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