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9
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Figures are disappeared from html report of SnpEff
HTML SnpEff
5 minutes ago by analyst ▴ 30
0
votes
1
reply
18
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Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment gaps
updated 10 minutes ago by ▴ 170 • written 48 minutes ago by • 0
0
votes
0
replies
12
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Highest variable features in single cell data
cell single
23 minutes ago by Kazo • 0
0
votes
0
replies
24
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Fetch table from clinvar database according to a list of rsid
clinvar fetching data python perl
57 minutes ago by ashaneev07 ▴ 20
0
votes
1
reply
96
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Network Alignment
plugin Cytoscape CytoMCS
updated 3 hours ago by ▴ 280 • written 22 hours ago by ▴ 40
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 3 hours ago by • 0 • written 2.4 years ago by • 0
0
votes
0
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36
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PCA plot
DESeq2 PCAplot
4 hours ago by Aaliya ▴ 10
0
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0
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32
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Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
4 hours ago by Ming Tommy Tang ★ 3.9k
0
votes
3
replies
230
views
Heatmap and rna-seq
RNA-Seq Heatmap and
updated 5 hours ago by 87k • written 2 days ago by ▴ 10
795
votes
167
replies
141k
views
109 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 3 months ago by 2.7k • written 7.4 years ago by 100k
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 5 hours ago by • 0 • written 8.3 years ago by • 0
0
votes
0
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53
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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
6 hours ago by 4fzcgueyp5 • 0
2
votes
3
replies
213
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 2 days ago by ★ 27k • written 2 days ago by ▴ 120
0
votes
1
reply
107
views
Annovar using R package
Annovar gnomAD R
updated 8 hours ago by 161k • written 11 hours ago by ▴ 40
0
votes
2
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135
views
Creating Synthetic Sequences for a ML Model
DNA ML
updated 9 hours ago by ★ 27k • written 12 hours ago by • 0
3
votes
8
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375
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 2 hours ago by 14k • written 1 day ago by ▴ 10
0
votes
6
replies
635
views
Adding CB tag to bam file
samtools bam
updated 11 hours ago by 14k • written 6 days ago by • 0
1
vote
10
replies
853
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
12 hours ago by DKA ▴ 40
0
votes
0
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63
views
Finding orthologs between genome error
OMA OMAbrowser
14 hours ago by hemantcnaik • 0
0
votes
2
replies
743
views
AGeNT LocatIt
AGeNT LocatIt WES UMI duplicates
updated 14 hours ago by ★ 2.1k • written 2.8 years ago by ▴ 10
0
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4
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156
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
just now by Bertalan_Takacs ▴ 90
0
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0
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76
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 12 hours ago by 43k • written 17 hours ago by • 0
0
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0
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66
views
News: 8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling DNAseq illumina RNAseq transcriptomics
17 hours ago by David Langenberger 11k
0
votes
0
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127
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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
17 hours ago by pramach1 ▴ 40
0
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14
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3.4k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 18 hours ago by • 0 • written 2.2 years ago by ▴ 10
0
votes
1
reply
103
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GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 15 hours ago by • 0 • written 19 hours ago by • 0
0
votes
0
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87
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
21 hours ago by salias • 0
4
votes
6
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290
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To get p-values for the TPM
P-value TPM RSEM
57 minutes ago by VITALA • 0
0
votes
2
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150
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 12 hours ago by 43k • written 22 hours ago by ▴ 10
0
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0
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78
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Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 12 hours ago by 43k • written 22 hours ago by • 0
1
vote
2
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127
views
alignment result
RNA-seq samtools hisat2
1 hour ago by ahmad.sajad4541 • 0
0
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0
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74
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News: hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models GLM R
updated 12 hours ago by 43k • written 1 day ago by ★ 2.5k
0
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0
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70
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Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet DoubletFinder Seurat modelHomotypic
updated 12 hours ago by 43k • written 1 day ago by • 0
0
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2
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181
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
18 hours ago by mropri ▴ 150
2
votes
2
replies
166
views
HaplotypeCaller - only SNPs
HaplotypeCaller GATK
updated 1 day ago by ▴ 30 • written 1 day ago by • 0
0
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0
replies
81
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
1 day ago by Kash ▴ 110
7
votes
2
replies
231
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by ▴ 390 • written 2 days ago by • 0
0
votes
1
reply
172
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting blast
updated 1 day ago by 100k • written 2 days ago by • 0
0
votes
4
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253
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 1 day ago by 14k • written 2 days ago by • 0
0
votes
1
reply
120
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 1 day ago by ★ 27k • written 1 day ago by • 0
0
votes
2
replies
204
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 12 hours ago by 43k • written 1 day ago by ▴ 140
2
votes
1
reply
179
views
Seurat merge and batch correction
Seurat
updated 1 day ago by 43k • written 2 days ago by ▴ 20
1
vote
1
reply
150
views
Herald: The Biostar Herald for Tuesday, April 23, 2024
herald
updated 1 day ago by 161k • written 1 day ago by 2.7k
1
vote
1
reply
124
views
Including plasmid in transcriptome assemblies
Bacteria BOWTIE2 Transcriptomics STAR
updated 1 day ago by 141k • written 1 day ago by • 0
2
votes
9
replies
797
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 1 day ago by 4.2k • written 6 months ago by • 0
0
votes
10
replies
362
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
1 day ago by atowns21 • 0
0
votes
1
reply
133
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 1 day ago by ★ 2.3k • written 1 day ago by • 0
3
votes
3
replies
196
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by 141k • written 1 day ago by • 0
0
votes
3
replies
215
views
Difference between samtools "-f 9" and "-f 11"
samtools sam bam
updated 1 day ago by 100k • written 1 day ago by • 0
1
vote
4
replies
219
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
updated 14 hours ago by 141k • written 1 day ago by ▴ 30
116,595 results • Page 1 of 2332
Recent Votes
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
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Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in by b.contreras.moreira ▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM by VITALA • 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result by ahmad.sajad4541 • 0
Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment by Scooter ▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host by ZhangYuanfeng • 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed) by Aaliya ▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95？ by Dateline • 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq by Kevin Blighe 87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies by Kevin Blighe 87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue by emmanouil.a ▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package by Pierre Lindenbaum 161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation by Lissa Cruz Saavedra • 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file by swbarnes2 14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
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