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187 results • Page 1 of 4
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38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 5 days ago by ▴ 170 • written 7.1 years ago by ▴ 240
22
votes
15
replies
10k
views
12 follow
Alternatives To Liftover
liftover genome mapping
updated 8 hours ago by • 0 • written 12.5 years ago by ▴ 170
19
votes
15
replies
2.3k
views
Forum: What is the amount of sequencing data produced annually?
data research sequencing
updated 2 days ago by • 0 • written 8 months ago by ▴ 70
19
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by ▴ 590
13
votes
18
replies
6.2k
views
9 follow
Blastn, need help to increase speed
RNA-Seq blastn blast+
updated 1 day ago by ★ 2.5k • written 3.2 years ago by ▴ 20
11
votes
9
replies
6.5k
views
6 follow
log2 fold change in RNA-seq analysis
fold log2 change
updated 4 minutes ago by 19k • written 2.4 years ago by ▴ 10
7
votes
13
replies
689
views
7 follow
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 minutes ago by 19k • written 29 days ago by ▴ 10
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 3 days ago by ▴ 30 • written 3.1 years ago by • 0
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq Zscore
updated 6 hours ago by ▴ 50 • written 6.5 years ago by ▴ 310
6
votes
4
replies
384
views
Details on salmon index
Salmon
updated 6 days ago by 6.6k • written 7 days ago by • 0
5
votes
4
replies
5.1k
views
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 4 hours ago by • 0 • written 3.9 years ago by ▴ 330
5
votes
3
replies
170
views
FastQC interpretation - 16S sequencing
interpretation amplicon Fastqc 16S
updated 22 hours ago by 142k • written 22 hours ago by ▴ 10
4
votes
9
replies
525
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
6 days ago by Gabriel R. ★ 2.9k
4
votes
9
replies
651
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 2 days ago by ▴ 130 • written 7 days ago by ▴ 20
4
votes
5
replies
4.5k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 6 days ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
4
votes
11
replies
929
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
1 day ago by J ▴ 10
3
votes
6
replies
324
views
Problem in getting geo file through GEOQUERY
geoquery Geo
updated 18 hours ago by 44k • written 1 day ago by ▴ 120
3
votes
5
replies
472
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
2 days ago by beantkapoor16 ▴ 10
3
votes
5
replies
439
views
Super ehancers
enhancers
updated 1 day ago by ★ 17k • written 21 days ago by • 0
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error MAUVE RAST genbank alignment
updated 12 hours ago by ▴ 40 • written 9.8 years ago by ▴ 70
3
votes
1
reply
145
views
vg autoindex seems stuck after a week of running
vg pangenome
updated 1 day ago by ▴ 380 • written 1 day ago by ▴ 10
3
votes
0
replies
117
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver ATAC-seq csaw
updated 1 day ago by 44k • written 1 day ago by ★ 1.2k
3
votes
4
replies
360
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq patch freeze genome
updated 5 days ago by 22k • written 7 days ago by • 0
3
votes
3
replies
267
views
getting exon coordinates
genomics
updated 6 days ago by 44k • written 7 days ago by • 0
3
votes
2
replies
201
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 1 day ago by 142k • written 2 days ago by ▴ 160
2
votes
3
replies
347
views
Trimming tool
Trimming
updated 2 days ago by 44k • written 5 days ago by • 0
2
votes
2
replies
258
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart RNAseq kallisto
6 days ago by bioinfo ▴ 150
2
votes
2
replies
302
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 6 days ago by 44k • written 6 days ago by ▴ 130
2
votes
11
replies
787
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
6 days ago by egascon • 0
2
votes
2
replies
208
views
Cannot install bwa-mem2 via conda
conda mamba python
updated 6 days ago by 44k • written 7 days ago by • 0
2
votes
4
replies
239
views
Filter Genome for Specific Sites
bedtools
updated 2 days ago by 44k • written 2 days ago by • 0
2
votes
6
replies
258
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes GATK SNP VCF
7 hours ago by anikcropscience ▴ 230
2
votes
4
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
2 hours ago by Aspire ▴ 330
2
votes
0
replies
135
views
Herald: The Biostar Herald for Monday, May 20, 2024
herald
2 days ago by Biostar 2.8k
2
votes
4
replies
250
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling GATK VCF
17 hours ago by Arton ▴ 10
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 2 days ago by 44k • written 5 months ago by 4.2k
2
votes
0
replies
191
views
Tool: Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap alignment NGMLR
4 days ago by micah ▴ 30
2
votes
3
replies
271
views
ggrepel function: geom_text_repel()
ggplot2 ggrepel R
updated 6 days ago by 44k • written 7 days ago by ▴ 20
2
votes
7
replies
597
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
updated 1 day ago by • 0 • written 6 weeks ago by ▴ 90
2
votes
1
reply
265
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 4 days ago by ★ 7.2k • written 5 days ago by • 0
1
vote
5
replies
347
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq deseq2
updated 6 days ago by 44k • written 7 days ago by • 0
1
vote
3
replies
557
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
updated 2 days ago by ▴ 160 • written 5 weeks ago by ▴ 40
1
vote
0
replies
177
views
News: Course on Manual Genome Curation
Genome-Assembly Pretext-View Manual-Genome-Curation
updated 6 days ago by 44k • written 6 days ago by ★ 2.5k
1
vote
6
replies
366
views
What marks a De-Novo Genome assembly as FAILED?
nanopore denovo illumina assembly genome
2 days ago by Umer ▴ 50
1
vote
1
reply
735
views
Herald: The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by 2.8k
1
vote
1
reply
214
views
constructing pangenome through psvcp
psvcp pangenome
4 days ago by analyst ▴ 50
1
vote
1
reply
197
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 6 days ago by ▴ 460 • written 17 days ago by ▴ 10
1
vote
16
replies
804
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
updated 4 days ago by 142k • written 7 days ago by • 0
1
vote
1
reply
230
views
mitochondrial genome assembly pipeline
mammals mitochondrial-genome
updated 6 days ago by 44k • written 7 days ago by ▴ 30
1
vote
4
replies
298
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA whole-genome-sequencing NCBI
updated 2 days ago by 44k • written 2 days ago by • 0
187 results • Page 1 of 4
Recent Votes
Comment: log2 fold change in RNA-seq analysis
Comment: log2 fold change in RNA-seq analysis
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
correct way of analyzing cell proportions in singlecell data
Comment: How to interpret this plotMDS of three disease clusters?
gseGO: no term enriched under specific pvalueCutoff
Answer: Error with BiocParallel. No barcodes files found
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Recent Replies
Answer: Z score by Akash D ▴ 50
I made this. Z scored on log2FC? will anyone support me on this? 3 groups A,B,C
Comment: log2 fold change in RNA-seq analysis by i.sudbery 19k
There is no such thing as a fold change of -2. Fold change is expression_in_condition_A/expresssion_in_condition_B as expression is a…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by i.sudbery 19k
DE with 100s of samples (particulalry if your experiemental design is more complex than 2 condition DE) can stretch consumer grade hardware…
Comment: Error with BiocParallel. No barcodes files found by NTerway • 0
Thank you for your help! I will try this out. I am trying to implement a collaborator's pipeline on my data and they only use SCE, scran an…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by ATpoint 82k
Once you have the counts any n is possible on a regular analysis-grade laptop or workstation. Even hundreds of samples. It's really the pre…
Comment: Error with BiocParallel. No barcodes files found by ATpoint 82k
You just tell the function to remove the prefix for you. Not on the actual file. Then you can add this information to the SCE, like `sce$da…
Comment: log2 fold change in RNA-seq analysis by May Ling • 0
Thank you for your response. I apologize if my understanding is incomplete. I would like to ask: if I have a fold change of -2, how can I c…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by i.sudbery 19k
Yeah, a standard 3x3 bulk experiement is very analysable on pretty much most good consumer laptops these days.
Comment: Error with BiocParallel. No barcodes files found by NTerway • 0
Thanks for the explanation! If I remove the prefix (GSM3972009_69_) then I will lose the sample annotation and cannot track them. I am more…
Comment: Unexpected read length from NGS by ATpoint 82k
Seconding this. Just ask them.
Answer: Error with BiocParallel. No barcodes files found by ATpoint 82k
The function assumes simply barcodes.tsv(.gz), genes.tsv(.gz) and matrix.mtx(.gz), without additional pre- or suffixes by default. You can …
Comment: Free AI for R programming by GenoMax 142k
Try: https://ai.tinybio.cloud/
Comment: How to interpret this plotMDS of three disease clusters? by ATpoint 82k
arrayWeights is imo always a good idea with human (or generally large) cohorts. What you can also do is to use something like sva to estima…
Comment: Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Po by GenoMax 142k
Not what you want to hear but it is possible that the Ab data is not good quality as the cellranger message says (assuming everything ran p…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by ATpoint 82k
Bulk RNA-seq is way less intensive in every regard than single-cell. Whatever you buy, be sure it's upgradable, meaning, no Mac :)
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