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96,223 results • Page 1 of 1925
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GROMACS ERROR
GROMACS
just now by Snigdha • 0
1
vote
2
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26
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How should I deal with my RNAseq result with high % of mutiple aligned reads?
RNAseq raw-count fastq
updated 5 minutes ago by 7.0k • written 1 hour ago by • 0
0
votes
1
reply
11
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Assign experimental groups and replicates within a GSE properly
R RNASeq GEO Datasets NCBI
updated just now by ▴ 80 • written 50 minutes ago by ▴ 20
0
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0
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10
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output as input new function
bash
54 minutes ago by gubrins ▴ 130
1
vote
2
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54
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Is there is any tools to calculate the Average Nucleotide Identity (ANI) among the Plasmodium genomes?
sequence ANI alignment calculator
1 hour ago by bhavya2269 • 0
0
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0
replies
12
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Homer - Finding Instance of Specific Motifs
bioinformatics analysis homer motif genomic
1 hour ago by SilviaT • 0
0
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0
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12
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CDSeq for deconvolution of whole blood RNAseq, any experience?
RNAseq Deconvolution
1 hour ago by Barista ▴ 10
0
votes
1
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51
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Huge single cell fastq dataset
sequencing cell single count fastq rna cellranger
updated 2 hours ago by ▴ 140 • written 2 hours ago by • 0
1
vote
2
replies
70
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Differential gene expression analysis in Python
python bioinformatics R
updated 1 hour ago by ▴ 300 • written 4 hours ago by ▴ 20
0
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4
replies
70
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Biosynthetic gene clusters
secondary-metabolite BGC bins metagenomics bacteria
1 hour ago by Elaine • 0
0
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2
replies
55
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shell --array in while loop
shell
1 hour ago by 82101202089 • 0
1
vote
1
reply
46
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extract uniprot id from pdb header file
from id extract file pdb header uniprot
updated 1 hour ago by 139k • written 3 hours ago by • 0
5
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10
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1.3k
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How to filter a VCF file with a list of CHR or contig IDs?
vcftools vcf chromosome contigs awk
updated 30 minutes ago by ★ 2.7k • written 16 months ago by ▴ 10
628
votes
157
replies
72k
views
93 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 10 days ago by 290 • written 4.9 years ago by 90k
1
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0
replies
26
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Blog: Using RNA-seq to understand plants and improve crop yield
BI Sequencing NGS RNAseq Bioinformatics
3 hours ago by Novogene ▴ 140
0
votes
3
replies
84
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Error in reading tab delimited file
R tab-delimited
updated 4 hours ago by 78k • written 5 hours ago by ▴ 60
13
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7
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426
views
7 follow
Should I buy a new apple M1-max with 64Gb Ram for single cell RNA seq analysis?
cell single seq M1 apple scRNA-seq max RNA
5 hours ago by tg02081300 ▴ 10
0
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2
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95
views
There is a problem with the BLASTN xml output
5 blast outfmt
2 hours ago by her • 0
0
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0
replies
51
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mtDNA-seq by Capture-based hybirdization library method
mtDNA
6 hours ago by Eric • 0
0
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0
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56
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calculate nucleotides frequencies from mapped reads in a BAM file
RNA-seq
6 hours ago by xiaoleiusc ▴ 70
2
votes
4
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135
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A bash question
bash
updated 1 hour ago by 46k • written 11 hours ago by ▴ 20
0
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3
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133
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Kmergenie：could find the best K value
Kmergenie
3 hours ago by 805251959 • 0
0
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0
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56
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convert monocle3 into monocle2 cds
monocle
10 hours ago by Bogdan ★ 1.1k
0
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1
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87
views
Trouble to generate genome indexes for human RNA-seq reads in STAR
STAR RNA-Seq
updated 9 hours ago by 108k • written 10 hours ago by • 0
0
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3
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139
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Noob: Help writing this shell for salmon quantification?
noob salmon rna seq
updated 5 hours ago by 17k • written 17 hours ago by • 0
0
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0
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33
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GWAS Analysis using Plink
GWAS PLINK
11 hours ago by 123 • 0
0
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0
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47
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DESeq2
DESEq2 rna-seq error
11 hours ago by rheab1230 ▴ 30
0
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0
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42
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Job: Postdoctoral Researcher (Maastricht University) in Bioinformatics to make FAIR data analysis real
FAIR-data Natural-Sciences Postdoc Health Bioinformatics
12 hours ago by secretariat-bigcat ▴ 10
0
votes
1
reply
91
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Circos plot of WGS assembly
circos plot
updated 14 hours ago by • 0 • written 1 day ago by ▴ 30
0
votes
1
reply
62
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How to assemble a genome from scaffolds to Chromosome level
genome assemble Scaffolds
updated 4 hours ago by ★ 1.8k • written 14 hours ago by ▴ 120
0
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0
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36
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How do you convert vcf file to a genotype file useable by eigenstrat
conversion vcf format eigenstrat
14 hours ago by RNAseqer ▴ 180
0
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0
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32
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VEP: "Given ref" field is empty when a ref. allele was in VCF input
WXS VCF VEP
14 hours ago by rebeliscu ▴ 30
0
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0
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42
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Samtools mpileup - I'm getting different number of base calls compared to number of quality scores
samtools R RNA-Seq mpileup Variant-Calling
13 hours ago by zuhaibzulfiqarahmed • 0
8
votes
16
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3.5k
views
Removing gaps from fasta sequence file
Python biopython
updated 2 hours ago by 19k • written 3.2 years ago by ▴ 30
0
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0
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39
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Parse paml output file in R
R beb paml
9 hours ago by el97004 ▴ 40
0
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0
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39
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Job: Pathogen Genomics Program Manager at UCSC's Genomics Institute
public health genomics bioinformatics
16 hours ago by genomicshr ▴ 30
0
votes
0
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36
views
Running RepeatMasker with RepeatModeler database
repeatmasker repeatmodeler
16 hours ago by pablo ▴ 200
2
votes
4
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99
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STAR alignment speed?
star alignment rna-seq
1 hour ago by a_bis ▴ 20
6
votes
7
replies
1.4k
views
Ensembl vep. How to filter population frequency less than 1%?
line Ensembl off vep
updated 18 hours ago by 108k • written 21 days ago by ▴ 10
0
votes
1
reply
60
views
Extract specific reads from fastq or SRA
reads filter fastq sra
updated 18 hours ago by 108k • written 18 hours ago by ▴ 290
1
vote
2
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308
views
[bam_sort_core] merging from 32 files and 16 in-memory blocks... samtools sort: failed to write header to "-"
samtools sort pacbio error
11 hours ago by eli_bayat ▴ 50
19
votes
16
replies
14k
views
10 follow
Cell Type Marker Databases?
database
updated 19 hours ago by 12k • written 9.5 years ago by ▴ 460
0
votes
0
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33
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Normalizing phosphoproteomics data
R phosphoproteomics normalize
19 hours ago by mm2568 • 0
0
votes
3
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191
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What is the most appropriate method for correlation analysis of mRNA-target correlations? And why?
data pearson spearman expression correlation kendall
updated 15 hours ago by 78k • written 20 hours ago by • 0
4
votes
13
replies
991
views
Tool: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
Pathview SBGN pathway analysis visualization Tool
updated 21 hours ago by • 0 • written 7 months ago by ▴ 410
0
votes
8
replies
227
views
error while plot data with deSeq2
DESeq2 RNA-Seq
2 hours ago by bioinformaticssrm2011 ▴ 100
0
votes
4
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134
views
bowtie2
genome mapping
3 hours ago by ponmalar1120 • 0
2
votes
3
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101
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Remove vector sequences from genome database
refseq univec vector database contamination
updated 22 hours ago by 108k • written 23 hours ago by ▴ 10
0
votes
1
reply
73
views
Heatmap for large significant data
pvalue data Heatmap large
updated 22 hours ago by 78k • written 22 hours ago by • 0
1
vote
3
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96
views
Paired-end SRA files t Fastq Files
ncbi analysis sequence sra next fastq-dump generation
updated 30 minutes ago by 108k • written 22 hours ago by • 0
96,223 results • Page 1 of 1925
Recent Votes
HOMER findMotifsGenome.pl to get the location of the motifs
Motif location for enriched motif in HOMER
A: Sra-Toolkit 2.3.1 Fastq-Dump Multiplefiles At Once Windows Command Line
GATK4,Cann't get right CalculateContamination result
Comment: How should I deal with my RNAseq result with high % of mutiple aligned reads?
A: Homer software -size parameter
Answer: Is there is any tools to calculate the Average Nucleotide Identity (ANI) among t
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Recent Replies
Comment: Assign experimental groups and replicates within a GSE properly by Basti ▴ 80
What is your expected metadata output ?
Comment: Reading in H5AD File from Human Cell Atlas by Soul writer • 0
thank you Eijy, i will try that way
Answer: How should I deal with my RNAseq result with high % of mutiple aligned reads? by Carlo Yague 7.0k
> % of Uniquely mapped reads is 32.37%, and I thought % of successfully > assigned alignments will be close to 32.37%, but only 10.1%. Why …
Comment: Paired-end SRA files t Fastq Files by GenoMax 108k
That information is in the [**SRA accession**][1] record. [1]: https://www.ncbi.nlm.nih.gov/sra/SRR592656
Comment: How to filter a VCF file with a list of CHR or contig IDs? by vkkodali ★ 2.7k
Sorry, I was wrong about the contents of the `fai` files -- the second column is the total length of the sequence. You can ignore the rest …
Comment: Variant annotation using VEP by prasundutta87 ▴ 580
You need to extract the AD field which means "Allelic depths for the ref and alt alleles in the order listed". You can access specific VCF …
Comment: How should I deal with my RNAseq result with high % of mutiple aligned reads? by benformatics ★ 2.6k
The dataset looks like it's total RNA so those reads are probably rRNA... why don't you check where the multi-mappers are aligning to the g…
Comment: Is there is any tools to calculate the Average Nucleotide Identity (ANI) among t by bhavya2269 • 0
Thank you for your suggestion.
Comment: Differential gene expression analysis in Python by fracarb8 ▴ 300
`scanpy` uses `diffxpy` to run DE analysis, BUT, keep in mind that `scanpy` is for single-cell RNA-Seq, not bulk.
Answer: Is there is any tools to calculate the Average Nucleotide Identity (ANI) among t by colindaven ★ 3.3k
There is a quick one here which doesn't do full alignments (might be less accurate, but fast). Usage may be appropriate depending on how ma…
Comment: A bash question by WouterDeCoster 46k
You don't need the samtools view there - you can pipe it straight to `samtools sort`
Comment: STAR alignment speed? by a_bis ▴ 20
Thank you for the advice. I'm very new to RNA-seq read alignment -- in your experience is there a particular thing I could do to improve al…
Comment: STAR alignment speed? by a_bis ▴ 20
Thanks, that's super helpful!
Comment: shell --array in while loop by 82101202089 • 0
Thank you very much! But, actually, I need to form a correspondence between the gene ID and the number for subsequent interconversion. Fo…
Comment: extract uniprot id from pdb header file by Pierre Lindenbaum 139k
what tried ?
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