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2
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2
replies
1.1k
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Sequence duplication FASTQC - genome sequencing
FASTQC WGS DNAseq
updated 3.2 years ago by 15k • written 3.2 years ago by ▴ 140
0
votes
0
replies
605
views
parsing blast xml to MSA/PSSM
biopython pssm blast xml MSA
3.2 years ago by patc • 0
0
votes
2
replies
840
views
Which tool for CRM enrichment?
CRM TFBS
3.2 years ago by Filago ▴ 110
0
votes
0
replies
677
views
Constituent enhancer .gff for ROSE algorithm from dREG output
super-enhancer enhancer dREG ROSE
3.2 years ago by c.heininger ▴ 10
4
votes
1
reply
1.0k
views
News: Online Course - A Practical Introduction to NGS Data Analysis (September 26-28, 2022)
workshop ngs data-analysis
updated 3.2 years ago by 45k • written 3.2 years ago by 11k
3
votes
1
reply
1.1k
views
Forum: Would an automated NGS analytics platform help research?
ngs data-analysis
updated 3.2 years ago by 45k • written 3.2 years ago by • 0
0
votes
0
replies
464
views
KEGG color mapper pathway missing
resonstruction Pathway
3.2 years ago by NATCHAPHON • 0
0
votes
1
reply
771
views
CLIP and CLASH data for miRNA-RNA interaction
RNA miRNA data_analysis CLIP CLASH
updated 3.2 years ago by ▴ 860 • written 4.0 years ago by • 0
0
votes
0
replies
486
views
species code
localblast
3.2 years ago by wes ▴ 90
1
vote
1
reply
988
views
bad CPU type error installing Bowtie2
bowtie2 monterey macos
updated 3.2 years ago by 153k • written 3.2 years ago by • 0
1
vote
2
replies
1.0k
views
How to remove miRNA duplicates and obtain read count
miRNA CD-HIT-DUP NGS CD-HIT
3.2 years ago by khq5801 ▴ 10
0
votes
0
replies
657
views
How to count mutations to check for transcription strand bias?
strand transcription bias mutations counting
3.2 years ago by n,n ▴ 390
0
votes
5
replies
2.0k
views
how can i add rsID(annotation) to my vcf file
VCF bcftools
updated 2.2 years ago by 45k • written 3.2 years ago by • 0
0
votes
1
reply
1.4k
views
peak calling in CUT&RUN(Chipseq) Analysis
cutandrun chipseq SEACR cutandtag deeptools
updated 3.2 years ago by ★ 1.9k • written 3.2 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Reference Annotation GTF that includes piRNAs?
piRNA GTF RNAseq
updated 3.2 years ago by ▴ 380 • written 3.2 years ago by • 0
1
vote
1
reply
711
views
Does DisGeNet propagate associations via disease ontology?
gene disgenet association disease
3.1 years ago by Yep ▴ 20
0
votes
2
replies
896
views
How solve solve error associated with cell clustering: quickCluster
scRNAseq
3.2 years ago by otieno43 ▴ 40
2
votes
4
replies
1.1k
views
Error to create a dds DESeq2 object.
DESeq2 RNAseq
3.2 years ago by cardon.chc • 0
0
votes
0
replies
459
views
how to format a large txt file to bed
methylation DNA bed
3.2 years ago by Super • 0
0
votes
2
replies
793
views
Population allele frequency
variant population Novel allele frequency
3.2 years ago by erzal.scarlett3 • 0
0
votes
2
replies
754
views
RNA-seq vs scRNA seq comparison
RNA-seq
3.2 years ago by abhay.kanodia ▴ 10
2
votes
2
replies
1.0k
views
read of insert VS circular consensus sequence
Long-read PacBio
3.2 years ago by arnauperis92 ▴ 10
0
votes
0
replies
1.3k
views
Job: Computational Biology Contract Position - Chinook Therapeutics, Inc.
Computational_Biology Genomics RNA-Seq Kidney
updated 2.7 years ago by 45k • written 3.2 years ago by ▴ 10
1
vote
5
replies
2.3k
views
GATK - GenomicsDBImport, ValidateVariant, CreateSequenceDictionary Issues
ValidateVariants HaplotypeCaller GATK GenomicsDB CreateSequenceDictionary
3.2 years ago by aheritas • 0
1
vote
1
reply
588
views
heatmap with multi NA/0 value
RNA-Seq NA heatmap
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 10
0
votes
0
replies
452
views
how to know about peak expression of gene
peak expression
3.2 years ago by aimanbarki ▴ 20
1
vote
2
replies
1.3k
views
Discrepancies between GO hits using GOATOOLS and the geneontology.org website
GO GOATOOLS gene-ontology
updated 2.2 years ago by 45k • written 3.2 years ago by ▴ 20
1
vote
1
reply
1.5k
views
add VAF to VCF
VCF VAF
updated 3.2 years ago by ▴ 840 • written 3.2 years ago by ▴ 20
2
votes
2
replies
1.1k
views
GEO Query error
GEOQuery
3.2 years ago by Ondina ▴ 100
5
votes
1
reply
1.2k
views
Compress already compressed file with bgzip without decompressing first
bgzip
updated 3.2 years ago by 2.9k • written 3.2 years ago by ▴ 10
1
vote
2
replies
868
views
Cleaning File system in bioinformatics
Filesystem
3.2 years ago by grant.hovhannisyan ★ 2.6k
0
votes
0
replies
432
views
Gene with low rate of benign mutations
Benign- mutation low rate
3.2 years ago by erzal.scarlett3 • 0
4
votes
13
replies
2.6k
views
6 follow
select rows in a tab-delimited ed file
linux text
updated 2.5 years ago by 45k • written 3.2 years ago by ▴ 60
1
vote
1
reply
782
views
Bacterial small-rna analysis
ngs bacteria small-rna
updated 3.2 years ago by ★ 2.0k • written 3.2 years ago by ▴ 70
5
votes
2
replies
3.3k
views
Forum: Skills for industry career in bioinformatics
industry
updated 3.2 years ago by 13k • written 3.2 years ago by ▴ 10
0
votes
2
replies
2.1k
views
Expected runtimes for GATK variant calling?
snp variant calling gatk
3.2 years ago by antmantras ▴ 80
0
votes
0
replies
632
views
How robust is rMATS when swapping samples?
splicing rmats RNA-seq STAR alternative
3.2 years ago by Apex92 ▴ 320
11
votes
13
replies
4.2k
views
Loop for removing the complete missing rows in a n number of groups of a dataframe in R
data-frame proteomics_data loop missing_value R
3.1 years ago by KABILAN ▴ 130
0
votes
7
replies
2.2k
views
Mapping reads using kallisto - rna seq analysis
rnaseq minconda analysis
3.2 years ago by bioinformatics ▴ 60
5
votes
4
replies
1.6k
views
Export list of full length DNA gene sequences
export dna browser genome sequence
3.1 years ago by David • 0
3
votes
6
replies
1.5k
views
Determine my species from Isolates assemblies
blast
updated 2.8 years ago by 45k • written 3.2 years ago by ▴ 50
1
vote
0
replies
837
views
Herald: The Biostar Herald for Monday, July 11, 2022
herald
3.2 years ago by Biostar 3.6k
4
votes
3
replies
1.2k
views
Rapid lookup of barcodes
levenshtein-distance NGS barcodes edit-distance
updated 3.2 years ago by 89k • written 3.2 years ago by ▴ 290
0
votes
1
reply
650
views
How Can I Find SNP id from Chromosome Position?
plink python gwas chromosome
updated 3.2 years ago by 166k • written 3.2 years ago by • 0
0
votes
0
replies
405
views
TCGA RNA-Seq data and set of conditions
RNA-Seq tcga conditions control
3.2 years ago by albacaro • 0
3
votes
1
reply
932
views
GO Term Analysis in scRNASeq data with low number of genes expressed
scrnaseq Seurat
updated 3.2 years ago by ★ 2.0k • written 3.2 years ago by ▴ 940
1
vote
1
reply
839
views
How to identify the genome build a dataset was aligned too?
grch ucsc hapmap genome build
updated 3.2 years ago by ★ 2.0k • written 3.2 years ago by ▴ 30
0
votes
0
replies
377
views
How to design ARM PCR primers for SNP detection?
ARM PCR Primers
3.2 years ago by Milad • 0
3
votes
11
replies
2.6k
views
RepeatMasker error
repeatmasking transciptome RNA-seq
updated 3.2 years ago by ★ 2.0k • written 3.2 years ago by ▴ 130
0
votes
5
replies
1.4k
views
NGS reads calculation
Galaxy
updated 2.7 years ago by 45k • written 3.2 years ago by ▴ 140
121,849 results • Page 400 of 2437
Recent Votes
Comment: Reading AD and other genotype information from the VCF file
C: How To Split A Bam File By Chromosome
DESeq2 time-series - full model matrix is less than full rank
Answer: RNAseq requirements: Biological and Technical replicates
C: Differential Peaks Between Replicates
Answer: DESeq2 time-series - full model matrix is less than full rank
Answer: DESeq2 time-series - full model matrix is less than full rank
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Recent Replies
Comment: Issue with renaming genes in expression matrix for heatmap in R by rfran010 ★ 1.6k
Maybe I'm missing something, it seems your recode function is switching values in a vector and then you later try to subset based on the ne…
Comment: Reading AD and other genotype information from the VCF file by Pierre Lindenbaum 166k
`bcftools query -f '[%CHROM %POS %REF %ALT %SAMPLE %GT %AD\n]' `
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by colindaven 7.8k
This one has the massive computing resources at the EBI behind it, so I wouldn't worry about capacity. Check their stats.
Answer: Cibersortx server down? by GenoMax 153k
Yes it is down now (though it was working ~ 3-4 hours ago): https://downforeveryoneorjustme.com/cibersortx.stanford.edu?proto=https
Answer: Available signature matrix for deconvoluting my bulk data using CIBERSORTX by Sam • 0
Have you checked out [cellxgene][1]? If you filter by organism you might find one that is suitable. [1]: https://cellxgene.cziscience.c…
Comment: RNAseq requirements: Biological and Technical replicates by jkim ▴ 220
Ouch, my mistake. Updated my comment.
Comment: RNAseq requirements: Biological and Technical replicates by i.sudbery 22k
However, one might argue that multiple biological samples (i.e. multiple blood draws) from each patient might be useful. Still, probably no…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by Mensur Dlakic ★ 29k
> So maybe this approach will help us find interesting and rare pathways — something along those lines. Still the same answer as before - …
Comment: ATAC-seq fragment size distribution - huge spike at 150 bp by yuntan1992 • 0
or add parameter "--soft-clipped-unmapped-tlen"
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions by ATpoint 89k
I would take this opportunity to encourage using different tools. Cibersortx is not open, its source code has never been published. That ha…
Answer: CIBERSORTx error: 'x' must be an array of at least two dimensions by catarinaventura_pt • 0
For those still looking for the answer about this, I just figured out that you need to have replicates for it to work.
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions by catarinaventura_pt • 0
I´m having the same problem here described. Any updates on how to solve this?
Answer: ATAC-seq fragment size distribution - huge spike at 150 bp by yuntan1992 • 0
After removing adapters with trim_galore, change the parameter of bowtie2 " --local" to "--end-to-end".
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by shevch2009 ▴ 20
That is a great comparison! :) It definitely looks that way. :) It's not about taxonomy, but about reconstructing metabolic pathways direc…
Comment: How to connect the UCSC when i get the DMR.plot? by Wren • 0
I tried using the main site but it still didn't work. Thanks anyway, I'll try other methods.
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