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25
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11
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3.7k
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Forum: Site Use Guidelines
meta biostars Guidelines
updated 14 hours ago by 43k • written 14.6 years ago by 100k
4
votes
11
replies
431
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 8 hours ago by 4.2k • written 1 day ago by • 0
0
votes
10
replies
315
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
6 hours ago by atowns21 • 0
2
votes
9
replies
750
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 8 hours ago by 4.2k • written 6 months ago by • 0
3
votes
8
replies
301
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 45 minutes ago by ★ 5.8k • written 1 day ago by • 0
3
votes
7
replies
425
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 14 hours ago by ★ 2.3k • written 6 weeks ago by • 0
0
votes
6
replies
375
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 1 minute ago by • 0 • written 22 days ago by ▴ 20
0
votes
6
replies
274
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
13 hours ago by Sd • 0
8
votes
5
replies
4.8k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
1
vote
5
replies
280
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
18 hours ago by anasjamshed ▴ 120
1
vote
5
replies
578
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 15 hours ago by • 0 • written 3 months ago by • 0
1
vote
4
replies
386
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus GTF
updated 5 hours ago by • 0 • written 5 months ago by • 0
0
votes
4
replies
197
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
updated 18 hours ago by 141k • written 20 hours ago by ▴ 20
0
votes
4
replies
211
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 10 hours ago by 14k • written 1 day ago by • 0
2
votes
4
replies
252
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
6 hours ago by HyperEvo • 0
5
votes
4
replies
573
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
4 hours ago by kirillkirilenko ▴ 40
2
votes
4
replies
200
views
interpretartion of a vcf file
calling genotype ONT variant diploid
1 hour ago by samuelkalandarov2002 ▴ 10
1
vote
3
replies
170
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
22 hours ago by WouterDeCoster 47k
0
votes
3
replies
181
views
Difference between samtools "-f 9" and "-f 11"
samtools sam bam
updated 11 hours ago by 100k • written 16 hours ago by • 0
0
votes
3
replies
172
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 20 hours ago by • 0 • written 23 hours ago by • 0
0
votes
3
replies
335
views
How to identify gaps in a genome?
awk seqkit assembly fasta genome
updated 21 hours ago by 6.4k • written 9 days ago by • 0
1
vote
3
replies
194
views
some error in building kraken2 database
metagenome kraken2
7 hours ago by Art1ess • 0
3
votes
3
replies
153
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 14 hours ago by 141k • written 15 hours ago by • 0
0
votes
2
replies
115
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage FASTA alignment identity
updated 1 hour ago by ▴ 170 • written 11 hours ago by ▴ 140
1
vote
2
replies
109
views
HaplotypeCaller - only SNPs
HaplotypeCaller GATK
updated 4 hours ago by ▴ 20 • written 9 hours ago by • 0
2
votes
2
replies
376
views
Using vg gamsort with naive sorting algorithm
gamsort vg
updated 19 hours ago by 161k • written 8 months ago by ▴ 80
0
votes
2
replies
53
views
To get p-values for the TPM
P-value TPM RSEM
2 minutes ago by VITALA • 0
7
votes
2
replies
185
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 10 hours ago by ▴ 390 • written 1 day ago by • 0
0
votes
1
reply
108
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 18 hours ago by ★ 2.3k • written 23 hours ago by ▴ 110
0
votes
1
reply
80
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
updated 15 hours ago by 161k • written 16 hours ago by ▴ 30
0
votes
1
reply
106
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 20 hours ago by 141k • written 20 hours ago by ▴ 20
0
votes
1
reply
92
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 14 hours ago by ★ 2.3k • written 14 hours ago by • 0
1
vote
1
reply
90
views
Including plasmid in transcriptome assemblies
Bacteria BOWTIE2 Transcriptomics STAR
updated 13 hours ago by 141k • written 13 hours ago by • 0
2
votes
1
reply
134
views
Seurat merge and batch correction
Seurat
updated 12 hours ago by 43k • written 1 day ago by ▴ 20
1
vote
1
reply
102
views
Herald: The Biostar Herald for Tuesday, April 23, 2024
herald
updated 12 hours ago by 161k • written 12 hours ago by 2.7k
0
votes
1
reply
171
views
Heatmap and rna-seq
RNA-Seq Heatmap and
updated 11 hours ago by 100k • written 1 day ago by ▴ 10
0
votes
1
reply
136
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting blast
updated 10 hours ago by 100k • written 1 day ago by • 0
0
votes
1
reply
110
views
Plots for DNA methylation data
plots DNA methylation
updated 21 hours ago by 141k • written 1 day ago by ▴ 10
0
votes
1
reply
80
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 5 hours ago by ★ 27k • written 11 hours ago by • 0
0
votes
1
reply
94
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
updated 5 hours ago by • 0 • written 10 hours ago by ▴ 150
1
vote
1
reply
134
views
WGCNA preservation analysis
WGCNA preservation
updated 23 hours ago by 54k • written 1 day ago by ▴ 180
1
vote
1
reply
139
views
Failed kmer content
kmer illumina ngs
updated 18 hours ago by 43k • written 1 day ago by • 0
0
votes
0
replies
59
views
The concept of co-occurrence network structure
co-occurence microbiome network
17 hours ago by ohtang7 ▴ 40
0
votes
0
replies
48
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
10 hours ago by Kash ▴ 110
0
votes
0
replies
46
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
4 hours ago by Aaliya • 0
0
votes
0
replies
9
views
Alternative splicing
single-cell suppa rnaseq splicing alternative
24 minutes ago by newuser2024 • 0
0
votes
0
replies
25
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet hetero Seurat modelHomotypic DoubletFinder
2 hours ago by Jeyong • 0
0
votes
0
replies
17
views
News: hands-on introduction to generalized linear models (GLMs) using R
GeneralizedLinearModels GLMs R
2 hours ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
19
views
alignment result
samtool RNA-seq analysis hisat2
1 hour ago by ahmad.sajad4541 • 0
0
votes
0
replies
64
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 18 hours ago by 43k • written 21 hours ago by • 0
57 results • Page 1 of 2
Recent Votes
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
C: RSeQC Output from infer_experiment.py - what does it mean?
Read pair orientation : Illumina TruSeq Stranded mRNA library
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Interested in Spatial Omics?
Answer: Seurat merge and batch correction
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Answer: To get p-values for the TPM by dsull ★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by dsull ★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file by samuelkalandarov2002 ▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by b.contreras.moreira ▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by yxwucq • 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error? by Mensur Dlakic ★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus by GenoMax 141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database by Art1ess • 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection by LauferVA 4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
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