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121,919 results • Page 67 of 2439
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0
votes
2
replies
673
views
Matrix for a Fisher's exact test
p-value fishers-test
updated 11 months ago by • 0 • written 11 months ago by • 0
3
votes
3
replies
797
views
Help With Sleuth
Sleuth RNASeq
updated 11 months ago by ★ 7.7k • written 11 months ago by • 0
1
vote
3
replies
803
views
ballgown shows very different results depending on number of groups prepared with hisat2-stringtie
ballgown stringtie
11 months ago by thomas.heigl.ibk • 0
0
votes
1
reply
598
views
DiffBind count function error related with BiocParallel and IRanges
dba chipseq iranges diffbind
11 months ago by buffealo ▴ 130
0
votes
1
reply
526
views
Gene expression relational database
relational-database gene-expression
updated 11 months ago by 45k • written 11 months ago by • 0
2
votes
3
replies
1.1k
views
Error during batch correction/PCA
RNA-seq batch-effect
11 months ago by Eduardo Oñate • 0
4
votes
7
replies
1.3k
views
Mendelian precison
CNV trios mendelian-precision
updated 11 months ago by 45k • written 11 months ago by ▴ 10
6
votes
6
replies
1.6k
views
Using BBtools to remove polyGs in Illumina data
bbtools
updated 11 months ago by 20k • written 11 months ago by ▴ 170
0
votes
2
replies
627
views
Clarification on UMI Length in FASTQ File after Trimming with fastp
umi adapter
updated 11 months ago by 153k • written 11 months ago by ▴ 10
0
votes
8
replies
1.3k
views
HTseq count issue, not aligning to features
htseq hisat2 rna-seq
11 months ago by boone5jones • 0
7
votes
11
replies
2.0k
views
Sankey + dot plot
R sankey gene-ontology GO
updated 11 months ago by ★ 3.1k • written 11 months ago by • 0
0
votes
3
replies
1.1k
views
How to convert CSV format to VCF using Python?
VCF CSV Python
updated 11 months ago by 45k • written 11 months ago by • 0
2
votes
4
replies
1.1k
views
When to use integration with scRNASeq
R SEURAT scRNA-seq
updated 11 months ago by 6.5k • written 11 months ago by ★ 1.3k
0
votes
0
replies
331
views
Annotating WGS Metagenome assemblies
metagenomics assembly metagenome annotation
11 months ago by naveedhasan2000 ▴ 10
4
votes
13
replies
2.3k
views
6 follow
featureCounts segmentation fault
featureCounts pipeline RNA-Seq
11 months ago by Jaber ▴ 30
3
votes
2
replies
741
views
how to get visium HD dataset with its information
spatial visiumHD transcriptomics scanpy
updated 11 months ago by ▴ 100 • written 11 months ago by • 0
6
votes
10
replies
3.0k
views
7 follow
Using GEOquery
R geo ncbi
updated 11 months ago by 45k • written 2.9 years ago by ▴ 40
0
votes
4
replies
1.6k
views
Performing Needleman-Wunsch Global Alignment for multiple mutant proteins against wild-type
Global-alignment Needleman-Wunsch
updated 11 months ago by 103k • written 12 months ago by ▴ 40
0
votes
2
replies
790
views
Merging bfiles
fam plink bfile bed
11 months ago by aj123 ▴ 130
1
vote
1
reply
571
views
Generally how are non-canonical chromosomes treated in human variation studies
variants SV assembly WGS
updated 11 months ago by 153k • written 11 months ago by ▴ 110
7
votes
8
replies
1.7k
views
Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, and intron only
rna-seq featurecounts
11 months ago by Ian 6.1k
0
votes
0
replies
416
views
Differences in DeepTools Heatmap Resolution Driven by Bed File
deeptools heatmaps ATACseq
11 months ago by gcooper1245 ▴ 10
19
votes
9
replies
2.7k
views
6 follow
Forum: The Evolution of NGS: What’s New and What’s Next?
ngs
updated 11 months ago by 153k • written 11 months ago by 5.9k
0
votes
0
replies
485
views
How to do multiz alignment locally
axtChain lastz multiz
updated 11 months ago by 153k • written 11 months ago by • 0
0
votes
0
replies
287
views
Significant difference in SNV count between replicates
VCF mutations WES SNV
11 months ago by dana • 0
0
votes
15
replies
2.4k
views
I have encountered some bugs in transcriptome analysis using STAR and RSEM.
STAR RSEM
updated 11 months ago by 56k • written 11 months ago by • 0
5
votes
5
replies
1.2k
views
How to compile Multiz
LastZ Github Multiz
updated 11 months ago by 166k • written 11 months ago by • 0
4
votes
2
replies
692
views
Converting bam to sam using htslib C++ api
bam htslib sam
updated 11 months ago by 166k • written 11 months ago by ▴ 80
1
vote
1
reply
1.1k
views
Visualizing Upregulated and Downregulated Genes in GO and KEGG Pathway Analyses
RNA-Seq
updated 11 months ago by ▴ 100 • written 11 months ago by ▴ 10
0
votes
0
replies
423
views
Issues with EnrichPathway Barplot in Reactome Pathway Analysis
RNA-Seq
11 months ago by roxana ▴ 10
0
votes
0
replies
513
views
VCF file missing MQRankSum and ReadPosRankSum for certain entries
snp vcf gatk
11 months ago by CRL-CHAR • 0
1
vote
2
replies
709
views
MarkDuplicatesSpark GATK flags for overcoming space issues
GATK
11 months ago by ChumBucket2024 ▴ 10
3
votes
6
replies
1.4k
views
FastQC and HISAT2
HISAT2 FastQC RNA-Seq
updated 11 months ago by 153k • written 12 months ago by ▴ 30
0
votes
0
replies
418
views
News: An Introduction to Nanopore direct RNA sequencing
cDNA RNA-seq Nanopore
updated 11 months ago by 45k • written 11 months ago by ★ 2.6k
0
votes
2
replies
790
views
Can't run CrossMap
CrossMap
11 months ago by Muhammad • 0
0
votes
2
replies
601
views
ChromHMM bed file annotation
Chromhmm annotation
11 months ago by sk_24 • 0
3
votes
2
replies
705
views
Numreads from samtools for Differential Expression
samtools featurecounts rna-seq deseq numreads
updated 11 months ago by 45k • written 11 months ago by • 0
1
vote
0
replies
694
views
Job: Graduate student positions (2-year Master's program) to conduct research in bioinformatics
graduate-student Masters-program
updated 11 months ago by 45k • written 11 months ago by ▴ 10
0
votes
0
replies
326
views
Confusing Pathway Analysis Results from DAVID
DAVID Reactome KEGG
11 months ago by saamhasan55 ▴ 10
0
votes
1
reply
629
views
Can someone install me (remotely) Amber24?
Amber24
updated 11 months ago by 45k • written 12 months ago by • 0
0
votes
5
replies
1.4k
views
Issue understanding ATAC-seq PCA
ATAC-seq PCA
updated 12 months ago by 5.1k • written 12 months ago by ▴ 10
0
votes
0
replies
389
views
ChromHMM
annotation promoter chromhmm
12 months ago by sk_24 • 0
0
votes
0
replies
313
views
Unable to analyse with cytoscape plugin bingo
Bingo
12 months ago by bookorg ▴ 20
3
votes
4
replies
922
views
No available matched normal for Mutect2 GATK
GATK
12 months ago by shems2001 • 0
1
vote
6
replies
1.4k
views
Kraken classified based on 1 mer
Kraken2
updated 12 months ago by 7.9k • written 12 months ago by • 0
2
votes
3
replies
1.4k
views
Choosing the Best Method for DEG Analysis: limma vs. DESeq2 for RSEM Normalized RNA-Seq Data
dese2 cbioportal RNA-seq limma
updated 11 months ago by 103k • written 12 months ago by ▴ 140
0
votes
2
replies
948
views
Trimmomatic 0.39 fails for adapters
Trimmomatic
updated 12 months ago by 103k • written 12 months ago by ▴ 130
0
votes
2
replies
989
views
Calculation of per-base average Quality (MAPQ, basecall quality Q20) from BAMs across multiple samples
MAPQ BAM coverage
12 months ago by Novice ▴ 10
4
votes
3
replies
989
views
Are tens of DEGs still biologically meaningful?
DEG differential-expression-analysis
updated 11 months ago by ▴ 290 • written 12 months ago by ▴ 20
4
votes
1
reply
641
views
Extract bam file to sam inside code?
bam sam
updated 12 months ago by 166k • written 12 months ago by ▴ 80
121,919 results • Page 67 of 2439
Recent Votes
A: Binning Over Genes And Calculating The Coverage [Bedops/Bedmap]
Answer: [vg giraffe] Unable to add read group to BAM file
Comment: [vg giraffe] Unable to add read group to BAM file
Answer: [vg giraffe] Unable to add read group to BAM file
Answer: vcf multisample
Answer: vcf multisample
Answer: vcf multisample
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Recent Replies
Comment: Help with species tree with orthofinder, iqtree and branch labeling by GenoMax 153k
> I don’t have clear species labels in my headers, only sequence IDs. I have not used iqtree, so this is only a thought ... should it be y…
Comment: Help with species tree with orthofinder, iqtree and branch labeling by san96 ▴ 190
Thank you so much.
Comment: [vg giraffe] Unable to add read group to BAM file by saruman ▴ 10
Yes, it seems so. Thank you.
Comment: cellranger mkref fail/error by GenoMax 153k
> The thing is that I do not have a genome for these organisms. That is not what `cellranger mkref` is expecting. You could consider alt…
Comment: cellranger mkref fail/error by tatsispolychronis • 0
The thing is that I do not have a genome for these organisms. i made a transcriptome using TRinity and this is what I am feeding it. I do n…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
Hi, I am not sure if i can call them good assemblies. Although based on QUAST and BUSCO stats, everything looks too good but somehow i hav…
Comment: cellranger mkref fail/error by GenoMax 153k
You need to provide the genome reference for the `--fasta` option as noted in https://www.10xgenomics.com/support/software/cell-ranger/late…
Answer: Methods to analyse structural similarity: co-evolution vs convergence by Joe 22k
Without historical data (ancient DNA) there's no way to ever really know this for certain. The best we can do is make inferences based on t…
Answer: vcf multisample by Pierre Lindenbaum 166k
eg : https://ega-archive.org/datasets/EGAD50000001683 > Merged VCF file from sporadic Meniere disease cohort (found using https://dat…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
Since this saga has been on going for a long time, it will be helpful to add a comment as to how you finally got to this point of what seem…
Comment: Methods to analyse structural similarity: co-evolution vs convergence by dthorbur ★ 3.1k
A few comments. 1. Coevolution of a trait between 2 organisms can end up with a convergent structure with another organism. It's not e…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
Thank you. Based on the description these two look really what i wanted to see.
Comment: miRNA low mapping ratings by i.sudbery 22k
Also, can you just clarify that the output above is from cutadapt or form miRDeep2?
Comment: miRNA low mapping ratings by i.sudbery 22k
What happens if you remove the `--minimum-length` requirement to cutadapt, and then run fastqc on the result - what size disitribution do y…
Answer: Genome Assembly QC from BAM files by colindaven 7.9k
You can have a look at the tools in the PAQman pipeline https://github.com/SAMtoBAM/PAQman, and maybe also Inspector https://github.com/Mag…
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