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181 results • Page 1 of 4
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22
votes
15
replies
10k
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12 follow
Alternatives To Liftover
liftover genome mapping
updated 4 days ago by • 0 • written 12.5 years ago by ▴ 170
20
votes
17
replies
13k
views
17 follow
Best Practice On Variant Discovery For Bacteria?
updated 3 days ago by • 0 • written 11.9 years ago by 33k
19
votes
10
replies
7.4k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by ▴ 590
19
votes
15
replies
2.3k
views
Forum: What is the amount of sequencing data produced annually?
data research sequencing
updated 6 days ago by • 0 • written 8 months ago by ▴ 70
13
votes
18
replies
6.2k
views
9 follow
Blastn, need help to increase speed
RNA-Seq blastn blast+
updated 5 days ago by ★ 2.5k • written 3.3 years ago by ▴ 20
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold log2 change
updated 3 days ago by • 0 • written 2.4 years ago by ▴ 10
8
votes
7
replies
3.9k
views
6 follow
What is the best practice of scRNA workflow for multiple patients and samples using Seurat
scRNA sing-cell RNA seurat integrate
updated 17 hours ago by ▴ 640 • written 3.5 years ago by ▴ 70
8
votes
9
replies
3.1k
views
7 follow
Venter Genome Vcf
vcf
updated 3 days ago by ▴ 20 • written 10.1 years ago by ▴ 980
7
votes
13
replies
846
views
7 follow
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 3 days ago by 19k • written 4 weeks ago by ▴ 10
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq Zscore
updated 4 days ago by ▴ 60 • written 6.5 years ago by ▴ 310
5
votes
3
replies
212
views
FastQC interpretation - 16S sequencing
interpretation amplicon Fastqc 16S
updated 4 days ago by 142k • written 4 days ago by ▴ 10
5
votes
3
replies
5.8k
views
Attempt to set 'rownames' on an object with no dimensions
R microbiome spieceasi
updated 20 hours ago by 142k • written 3.6 years ago by ▴ 30
5
votes
4
replies
5.2k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 4 days ago by • 0 • written 3.9 years ago by ▴ 330
4
votes
6
replies
12k
views
Looking for differential gene expression between treatment, within a specific cluster (seurat)
seurat
updated 13 hours ago by ★ 17k • written 4.7 years ago by ▴ 230
4
votes
6
replies
431
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body expression atlas
3 days ago by Shicheng Guo ★ 9.4k
4
votes
9
replies
674
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 6 days ago by ▴ 130 • written 11 days ago by ▴ 20
4
votes
6
replies
329
views
Error with BiocParallel. No barcodes files found
Barcodes scRNA-seq SingleCellExperiment
3 days ago by bio_info ▴ 20
4
votes
1
reply
233
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq padj p-value
updated 3 days ago by 14k • written 3 days ago by • 0
4
votes
11
replies
966
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
5 days ago by J ▴ 10
4
votes
2
replies
211
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq stringtie indexing salmon
updated 2 days ago by 6.6k • written 2 days ago by ▴ 10
3
votes
5
replies
486
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
5 days ago by beantkapoor16 ▴ 10
3
votes
2
replies
181
views
How to interpret this plotMDS of three disease clusters?
microarray plotMDS DEGs
updated 4 days ago by 82k • written 4 days ago by • 0
3
votes
5
replies
353
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 1 day ago by 162k • written 3 days ago by • 0
3
votes
2
replies
187
views
Multiplexing for pooled CRISPR screen sequencing
multiplex CRISPR-screen Illumina
4 days ago by Tuấn Anh • 0
3
votes
4
replies
478
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 3 days ago by ★ 1.7k • written 10 days ago by ▴ 130
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error MAUVE RAST genbank alignment
updated 4 days ago by ▴ 40 • written 9.8 years ago by ▴ 70
3
votes
3
replies
229
views
Unexpected read length from NGS
NGS Illumina
3 days ago by QX • 0
3
votes
6
replies
353
views
Problem in getting geo file through GEOQUERY
geoquery Geo
updated 4 days ago by 44k • written 5 days ago by ▴ 120
3
votes
0
replies
126
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver ATAC-seq csaw
updated 5 days ago by 44k • written 5 days ago by ★ 1.2k
3
votes
4
replies
345
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm ChIP-seq consensus peaks
23 hours ago by Alexandra • 0
3
votes
4
replies
160
views
Invalid CIGAR after using bam clipOverlap
validatesamfile cigar bam clipoverlap
5 hours ago by MboiTui ▴ 20
3
votes
7
replies
4.0k
views
Difference in Bismark output methylation call files and coverage files
RRBS Bismark DNA-methylation
updated 3 days ago by ★ 2.9k • written 3.9 years ago by ▴ 40
3
votes
2
replies
217
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 5 days ago by 142k • written 5 days ago by ▴ 160
3
votes
0
replies
153
views
Herald: The Biostar Herald for Monday, May 20, 2024
herald
6 days ago by Biostar 2.8k
3
votes
1
reply
168
views
vg autoindex seems stuck after a week of running
vg pangenome
updated 5 days ago by ▴ 380 • written 5 days ago by ▴ 10
3
votes
8
replies
880
views
Random Access remote BAM files
htslib BAM
updated 4 days ago by • 0 • written 3 months ago by ▴ 20
3
votes
5
replies
453
views
Super ehancers
enhancers
updated 5 days ago by ★ 17k • written 25 days ago by • 0
2
votes
11
replies
745
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r ComplexHeatmap
updated 22 hours ago by 44k • written 9 days ago by • 0
2
votes
4
replies
250
views
Filter Genome for Specific Sites
bedtools
updated 6 days ago by 44k • written 6 days ago by • 0
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 6 days ago by 44k • written 5 months ago by 4.2k
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
4 days ago by Aspire ▴ 330
2
votes
5
replies
305
views
Z score
Z-score
updated 3 days ago by 44k • written 4 days ago by ▴ 60
2
votes
6
replies
394
views
Harmony integration group.by.var parameter
single-cell harmony
updated 14 hours ago by ★ 17k • written 3 days ago by ▴ 640
2
votes
3
replies
255
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity mtDNA PacBio
3 days ago by hashim.rana11 ▴ 20
2
votes
4
replies
276
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling GATK VCF
4 days ago by Arton ▴ 10
2
votes
1
reply
186
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF gnomAD SNP
updated 2 days ago by 22k • written 2 days ago by ▴ 10
2
votes
7
replies
609
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
updated 5 days ago by • 0 • written 6 weeks ago by ▴ 90
2
votes
0
replies
214
views
Job: Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics Sequencing Sweden Stockholm SciLifeLab
3 days ago by Matthias Zepper 4.6k
2
votes
3
replies
358
views
Trimming tool
Trimming
updated 6 days ago by 44k • written 9 days ago by • 0
2
votes
6
replies
320
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes GATK SNP VCF
4 days ago by anikcropscience ▴ 230
181 results • Page 1 of 4
Recent Votes
C: snpEff assigned all variants as modifier intergenic
A: Problem in indexing toplevel genome with HISAT2
C: The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
Comment: How do we do quantification using stringtie merge option for all the merged samp
Answer: bcftools view error: the tag "mis" is not defined in the VCF header
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Recent Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by ATpoint 82k
Why is your `GeneName` column in mapped a mix of Ensembl IDs and gene names? What Jared wants to say is that during the preprocessing you s…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID by GenoMax 142k
> only give me partial results It is possible that not every Ensembl ID is going to convert to Entrez ID. Have you tried: https://www.b…
Comment: BAM to Bedgraph creating an empty file by raphael.B ▴ 520
You have a space in your reference path. Not sure it's intended?
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID by Anya • 0
Do you have any recommendations of such sources or how to search for them? I'm a newbie and I need to convert GRCh38 Ensembl IDs to Entrez …
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID by Shred ★ 1.4k
Genecards added a footer saying that >SCRAPING AND OTHER AUTOMATED DOWNLOAD AND USE OF GENECARDS DATA STRICTLY PROHIBITED While this is …
Comment: perl Error - needLargeMem Bigwig by marco.barr ▴ 130
I managed to correct and solve the problem. It was due to issues with memory parameter settings on different login nodes. Additionally, I h…
Answer: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID by Anya • 0
Here's a slightly changed version of this script. I changed line 42 from `'title':'NCBI Entrez Gene'` to `'title':'NCBI Gene'` ). And…
Comment: How do we do quantification using stringtie merge option for all the merged samp by Varsha • 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8? by Asaf 10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
Answer: Tools for chromosomal aneuploidy detection by a.alnawfal.1992 ▴ 260
As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosom…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Sara ▴ 30
I used Seurat, and in Seurat, I have gene names (which some are with gene-symbols and some with ENSG ids). Then I did Pseudobulk. how can …
Comment: How to decrease the motif score? by ATpoint 82k
So you scan the entire genome and got nothing significant? Is that the issue?
Comment: perl Error - needLargeMem Bigwig by b.contreras.moreira ▴ 200
A quick search suggests the problem is your empty input file? See <https://biostar.galaxyproject.org/p/6794>
Comment: Invalid CIGAR after using bam clipOverlap by MboiTui ▴ 20
ooh good pickup. Might not be the problem but definitely not helping. Will re-run with streamlined workflow and with double quotes and see …
Comment: Invalid CIGAR after using bam clipOverlap by Pierre Lindenbaum 162k
may be not the problem but why this ` RG:Z:H7J22DRX3.${lane}-1C23074F ` in the RG. you're using single quotes with bwa-mem and it won't …
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