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122,012 results • Page 603 of 2441
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2
votes
3
replies
2.7k
views
Velocyto for smart seq2 taking an excessively long time (and memory)?
velocyto slurm RNAvelocity smart-seq2
4.2 years ago by skjw1029 ▴ 80
3
votes
3
replies
1.5k
views
Is there an online server to get a great phylogenetic tree?
phylogenetic tree
updated 4.2 years ago by ★ 30k • written 4.2 years ago by ▴ 10
0
votes
2
replies
1.2k
views
BCFtools -R stopped working
BCFtools
4.2 years ago by julia.zollner ▴ 20
2
votes
3
replies
1.5k
views
VG Installation with Ubuntu
vg vgteam
4.2 years ago by jdrubin • 0
2
votes
0
replies
1.0k
views
eggNOG v5 annotation file
eggNOG Annotation
4.2 years ago by Mehmet ▴ 820
0
votes
2
replies
1.7k
views
Jellyfish histo produces a blank file
genome jellyfish
updated 2.5 years ago by 45k • written 5.6 years ago by • 0
1
vote
0
replies
791
views
Weighted random walk in R
Walk Ranwom R Graph
4.2 years ago by Filago ▴ 110
5
votes
6
replies
3.1k
views
How to replace multiple string columns to binary values (0 and 1) in a dataframe?
dataframe R
updated 4.2 years ago by 21k • written 4.2 years ago by • 0
0
votes
19
replies
4.1k
views
error related to vcfstats
numpy snp vcf vcfstats
4.2 years ago by rheab1230 ▴ 150
0
votes
0
replies
510
views
differential gene expression analysis with Downstream analysis
TCGABiolinks Bioconductor
4.2 years ago by Gisele • 0
0
votes
0
replies
640
views
Comparing expression of a gene from different datasets in cBioportal
cbioportal expression median
4.2 years ago by Lordegod • 0
1
vote
4
replies
1.7k
views
convert detailed alignment format to fasta
alignment
updated 2.3 years ago by 45k • written 4.2 years ago by ▴ 10
3
votes
4
replies
3.9k
views
PLINK ASSOC : Skipping --assoc/--model since less than two phenotypes are present.
ASSOC PLINK phenotypes
4.2 years ago by Michal Nevo ▴ 140
0
votes
0
replies
853
views
Job: Bioinformatics Specialist - Torii Lab @ University of Texas at Austin (Texas, US)
NGS plants R
updated 2.6 years ago by 45k • written 4.2 years ago by • 0
0
votes
0
replies
947
views
Job: Postdoctoral Associate - Kuriyan Lab @ University of California, Berkeley (California, US)
biophysics biochemistry
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
0
votes
0
replies
755
views
Intersecting phyloP bed and per-base bed files
format bedtools bed
4.2 years ago by gokberk ▴ 90
0
votes
1
reply
978
views
Job: Computational Biologist - Versiti Blood Research Institute, Milwaukee, WI, USA
computational-biologist
updated 2.3 years ago by 45k • written 4.2 years ago by • 0
0
votes
0
replies
631
views
Reducing the background noise of gene expression data
expression alzheimer dataset noise gene
4.2 years ago by Aram • 0
0
votes
2
replies
1.5k
views
individual-level allele frequencies
allele frequencies clustering plink
updated 4.2 years ago by 11k • written 5.1 years ago by ▴ 220
3
votes
11
replies
3.6k
views
I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv.
mem samtools bwa
updated 4.2 years ago by ★ 1.3k • written 4.2 years ago by • 0
0
votes
4
replies
2.7k
views
Is it possible for a cell cluster to not have cells of a certain condition?
seurat
updated 2.6 years ago by 45k • written 4.2 years ago by • 0
1
vote
4
replies
3.8k
views
Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (84, 195)
ATAC-seq PICARD
4.2 years ago by bill • 0
0
votes
2
replies
976
views
Mapping taxonomy ID to virus host
host viruses taxid
4.2 years ago by Jagoda • 0
0
votes
3
replies
1.5k
views
Variant annotation using VEP
Annotation Zygosity VEP
updated 4.0 years ago by ▴ 20 • written 4.2 years ago by ▴ 40
124
votes
13
replies
187k
views
13 follow
How Can I Convert Bam To Sam?
bam next-gen-sequencing sam
updated 2.1 years ago by 45k • written 15.3 years ago by 5.0k
0
votes
0
replies
900
views
Herald: The Biostar Herald for Tuesday, August 03, 2021
herald
4.2 years ago by Biostar 3.6k
0
votes
2
replies
1.1k
views
Finding Molecular function for more than 100 GO terms
Gene Ontology
updated 4.2 years ago by 27k • written 4.2 years ago by ▴ 20
0
votes
0
replies
538
views
Is there any index could evaluate the polymorphic genes with SNPs and Indels in population ？
population polymorphism
4.2 years ago by Damon_Wan • 0
6
votes
11
replies
3.9k
views
Python fast way to get ONLY MAIN metadata for GSE ? (not walking through thousands underlying GSM-samples : slow or even endless)
GEO GEOparse
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 220
0
votes
0
replies
691
views
Calculating RMSD
RMSD alignment align protein
4.2 years ago by antoniaa ▴ 30
0
votes
1
reply
1.7k
views
How to download all sequences of a whole genome shotgun sequencing (WGS) project
seqrecords wgs ncbi
updated 4.2 years ago by ▴ 390 • written 4.2 years ago by ▴ 20
1
vote
0
replies
837
views
Job: Manager of Bioinformatics at Mogrify
Manager Python NGS SingleCellSequencing
4.2 years ago by Mogrify Talent Acquisition ▴ 10
1
vote
3
replies
2.5k
views
RNA-seq doesn't match qPCR and western blot results
qPCR siRNA RNA-seq
updated 4.2 years ago by ▴ 390 • written 4.2 years ago by ▴ 10
0
votes
1
reply
864
views
Obtaining mapped reads after extracting unmapped reads .
Unmapped samtools BAM
4.2 years ago by shrivadeepak • 0
2
votes
3
replies
1.3k
views
Using psi-blast to obtain all members of the protein family
psi-blast blast
updated 4.2 years ago by 9.0k • written 4.2 years ago by ▴ 30
0
votes
0
replies
440
views
Is it possible to analyze only a subset of genes from different microarray datasets?
microarray
4.2 years ago by iltan1 • 0
0
votes
0
replies
633
views
infer the orientation of z score by using the harmonisation codes
Gwas MR
4.2 years ago by celia • 0
50
votes
16
replies
15k
views
12 follow
Tool: Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr software ngs
updated 2.3 years ago by 45k • written 12.1 years ago by ▴ 450
0
votes
1
reply
998
views
Syngeneic mouse model Database with RNA-seq data?
RNA-seq mouse tumor
4.2 years ago by Lesdormis • 0
1
vote
5
replies
3.8k
views
FastUniq error - Error in open left fastq file site1_R1_P_qtrim.fq for read!
software error fastuniq assembly
updated 7.4 years ago by 154k • written 7.4 years ago by ▴ 30
0
votes
0
replies
566
views
Pan-cancer over-expressed or down-regulated gene list
TCGA expression
4.2 years ago by Shicheng Guo ★ 9.6k
0
votes
4
replies
4.1k
views
Help with Pathway annotation after Seurat DE analysis
Seurat enrichment DE Pathway
4.2 years ago by mshubham • 0
0
votes
0
replies
738
views
Annovar output no comment column?
annovar GWAS annotation Annovar Post-GWAS
4.2 years ago by okiedokie1208 ▴ 40
1
vote
9
replies
4.3k
views
Help with Volcano plot
Volcano r plot ggplot
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
7
votes
5
replies
1.9k
views
Orthology, sequence similarity, and conservation of function
homology function similarity prediction sequence orthology
4.2 years ago by Dunois ★ 2.9k
0
votes
1
reply
912
views
PHYLIP file has not seq text.
iqtree alignment Vcf vcf2phylip
updated 4.2 years ago by ▴ 220 • written 4.2 years ago by • 0
0
votes
0
replies
771
views
Building vcf from most common alleles
vcf consensus variant
4.2 years ago by Eugene • 0
0
votes
0
replies
775
views
Does anyone have any experience in hacking MaxBin2 to handle custom marker sets?
metagenomics maxbin2 binning
4.2 years ago by O.rka ▴ 750
1
vote
0
replies
989
views
Blog: Revisiting bulk RNA-Seq applications
RNASeq variants TWAS Neoantigens
updated 2.3 years ago by 45k • written 4.2 years ago by ▴ 340
0
votes
5
replies
1.4k
views
How would I go about picking out certain files in a FASTA file and putting them in a new, separate file?
MSA fasta dataset multiple_sequence_alignment
4.2 years ago by crisstyl ▴ 10
122,012 results • Page 603 of 2441
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Answer: Recommendations for 200 SNP markers genotyping
Comment: Reasonable number of SNPs in a bacterial genome.
The Biostar Handbook. A bioinformatics e-book for beginners.
Genome Assembly QC from BAM files
Answer: Scaling RNA-Seq data before clustering?
Answer: Scaling RNA-Seq data before clustering?
Online course: RNA sequencing data analysis using R and Bioconductor - 3–14 November
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Recent Replies
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome. by michael.ante ★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Ram 45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info by ATpoint 89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by ATpoint 89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks by rfran010 ★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample by cmdcolin ★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by aj123 ▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
This statement makes zero sense in response to what I wrote.
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