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2
votes
2
replies
974
views
Proper HTSeq usage on bacterial genome. Don't quite understand --t
RNAseq HTSeq
23 months ago by SushiRoll ▴ 140
0
votes
0
replies
658
views
CNVkit interpretation: copy number calculation with the correspondence to the unknown ploidy
CNV CNVkit
23 months ago by rbioinfo ▴ 40
2
votes
7
replies
1.7k
views
Salmon and SPAdes contigs filtering
salmon SPAdes
23 months ago by Skeetul ▴ 10
3
votes
1
reply
1.1k
views
Using DADA2 for finding viral sequence variants
RNASeq Amplicon dada2 Variant
updated 23 months ago by 3.4k • written 23 months ago by ▴ 50
0
votes
0
replies
447
views
Method for detecting X-chromosome aneuploidy from SNP array data
SNP aneuploidies
23 months ago by Apprentice ▴ 190
0
votes
1
reply
1.0k
views
Does Guppy have no --fast_out parameters?
Guppy fast5 ONT
updated 23 months ago by 45k • written 23 months ago by • 0
1
vote
0
replies
471
views
How to find OS duration, status information of patients in GSE1159 (Microarray data analysis)
Microarray
23 months ago by sf.jeong510 ▴ 10
0
votes
1
reply
570
views
How to merge my vcf files (n=6) with existing Pf6 vcf file and do pca?
Pf6
updated 23 months ago by 103k • written 23 months ago by • 0
1
vote
3
replies
1.1k
views
Visium data analysis software supporting deconvolution analysis
Visium
updated 23 months ago by ▴ 10 • written 23 months ago by ▴ 60
1
vote
4
replies
1.2k
views
Visium deconvolution reference datasets
Visium-deconvolution spatial
updated 23 months ago by ▴ 10 • written 23 months ago by ▴ 60
0
votes
1
reply
781
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup RNA Rsamtools seq
updated 23 months ago by ★ 2.4k • written 23 months ago by • 0
17
votes
8
replies
14k
views
9 follow
Combining Microarray and RNAseq data
RNA-Seq normalization R microarray
updated 23 months ago by ▴ 80 • written 9.9 years ago by ★ 1.2k
0
votes
0
replies
645
views
News: Course -Metabarcoding in Microbial Ecology
R Qiime2 Microbial-Ecology Metabarcoding
updated 23 months ago by 45k • written 23 months ago by ★ 2.6k
1
vote
3
replies
1.3k
views
No hits for influenza virus in an RNA seq. data using FAST Q screen (from babraham institute)
alignment Linux mapping
updated 23 months ago by ▴ 420 • written 23 months ago by ▴ 30
0
votes
0
replies
507
views
Combining ComBatseq to remove batch effects and fragment size normalization
ComBatseq FPKM
23 months ago by Hamza ▴ 10
8
votes
14
replies
3.0k
views
6 follow
Bioinformatics software for single cell omics
single-cell
23 months ago by jackson9 ▴ 10
0
votes
5
replies
1.3k
views
I cannot obtain summary alignment with Bowtie2
Bowtie2 alignmentsummary SmallRNASeq
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
0
votes
6
replies
2.0k
views
Cannot find summary message after Bowtie2 mapping
Bowtie2
updated 23 months ago by 9.0k • written 3.7 years ago by ▴ 10
3
votes
11
replies
17k
views
Merging multiple samples in Seurat
scRNA-seq snRNA-seq RNA-seq Seurat
updated 14 months ago by ▴ 10 • written 23 months ago by ▴ 10
2
votes
1
reply
1.1k
views
Extracting most significant core enrichment genes after performing GSEA
R GSEA
updated 23 months ago by ★ 3.1k • written 23 months ago by • 0
0
votes
1
reply
756
views
Does GATK SetNmMdAndUqTags reduces the size of a CRAM?
CRAM WGS sam GATK SetNmMdAndUqTags
updated 23 months ago by 166k • written 23 months ago by • 0
1
vote
0
replies
706
views
Job: Research technician and a Postdoc on pediatric leukemias at the Ding Lab of Johns HopkinsMedicine
Pediatric Leukemias Postdoc
13 months ago by alwayshope ▴ 40
5
votes
9
replies
2.2k
views
Wildcards in Snakemake
Python workflow Snakemake wrapper
updated 23 months ago by 23k • written 23 months ago by ▴ 210
1
vote
2
replies
1.4k
views
Which embedding for clustering of cells in single-cell RNAseq?
UMAP PCA ICA clustering tSNE
4 months ago by e.r.zakiev ▴ 260
0
votes
0
replies
693
views
Job: Postdoctoral Fellow- Behavior and Circuit Neuroscience at Dr. JuarezLab of University of Maryland-Baltimore
Neuroscience Postdoc
23 months ago by alwayshope ▴ 40
1
vote
5
replies
3.0k
views
How to install Guppy from Nanopore Technologies?
Guppy fast5 ONT
updated 23 months ago by 45k • written 23 months ago by • 0
0
votes
0
replies
542
views
DE analysis in paired samples with limma
R DE limma
23 months ago by dv_f • 0
1
vote
3
replies
1.9k
views
Computing Tajima's D from haploid SNPs
Haploid SNPs
updated 23 months ago by ▴ 290 • written 4.3 years ago by ▴ 50
5
votes
1
reply
1.5k
views
Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance
vg pggb giraffe
updated 23 months ago by ▴ 760 • written 23 months ago by ▴ 30
5
votes
2
replies
3.5k
views
Samtools fails with libcrypto error
RNAseq Qualitycheck samtools BAM
updated 23 months ago by 103k • written 23 months ago by ▴ 10
0
votes
0
replies
635
views
Minimum spanning tree based on cgMLST allelic profiles
cgMLST spanning Minimum tree
23 months ago by blur ▴ 280
0
votes
2
replies
695
views
I'm doing RNA seq but the quality control sequence GC contens shape looks weird...
RNAseq fastqc GCcontents Riunx
updated 23 months ago by ★ 19k • written 23 months ago by ▴ 10
1
vote
3
replies
3.7k
views
DESeq2 lfcshrink, shrinkage apeglm vs normal
DESeq2 RNA-seq DEG shrinkage
updated 23 months ago by 3.4k • written 23 months ago by ▴ 70
2
votes
4
replies
1.3k
views
Normal vs Tumor - Kaplan Meier Survival Analysis
fpkm Survival-Analysis rpkm
updated 23 months ago by 45k • written 23 months ago by • 0
0
votes
4
replies
977
views
Fast QC results (per sequence GC content) - RNA seq
FastQC RNA-seq
23 months ago by comu • 0
1
vote
5
replies
2.7k
views
what is the output of 'samtools coverage'
bam samtools coverage bamfiles
updated 23 months ago by 166k • written 23 months ago by ▴ 20
4
votes
2
replies
1.0k
views
How to interpret the Variant Allele Frequency??
VarScan Variant-allele-frequency
updated 23 months ago by ★ 4.4k • written 24 months ago by ▴ 40
0
votes
1
reply
641
views
Hisat2-build (5.ht2 and 6.ht2 are missing)
hisat2
updated 23 months ago by 45k • written 23 months ago by • 0
4
votes
4
replies
2.0k
views
Mitochondrial contig identification in fungal genome assemblies
genome assembly fungi mitochondria
23 months ago by VineethVenumadhavan ▴ 50
2
votes
4
replies
1.7k
views
BBtools callvariants.sh
SNP bbtools alignment
updated 23 months ago by 20k • written 2.3 years ago by ▴ 80
4
votes
6
replies
4.4k
views
6 follow
How to discard alignments from SAM/BAM file that have mismatches
BAM SAM minimap nanopore
updated 23 months ago by 20k • written 2.3 years ago by ▴ 50
0
votes
3
replies
1.4k
views
Deduplication
UMI UMI_TOOLS removal Deduplication PCR-duplicate
updated 23 months ago by 20k • written 2.2 years ago by • 0
3
votes
8
replies
4.4k
views
Aligning very short sequences using bowtie2, I need fine control over how many mismatches are allowed. Adjust scoring?
bowtie2
updated 23 months ago by 20k • written 2.2 years ago by ▴ 20
0
votes
0
replies
494
views
find_marker_genes throws error using case_groups and control_groups
stereopy python find_marker_genes
23 months ago by Chirag Nepal ★ 2.4k
0
votes
0
replies
485
views
How to adjust kaplan-meier curves for confounding factors and get p value?
kaplan-meier coxph confounding survivalanalysis
23 months ago by Manuel ▴ 10
0
votes
0
replies
464
views
Best way for risk scoring a single sample
cancer risk-score meta-analysis
updated 23 months ago by 45k • written 23 months ago by • 0
0
votes
6
replies
1.3k
views
Allele numbers and frequencies in X and Y chr?
chr-X
updated 23 months ago by 20k • written 23 months ago by • 0
5
votes
8
replies
2.8k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 23 months ago by ▴ 10 • written 5.1 years ago by ▴ 250
1
vote
1
reply
1.8k
views
A suited tool to guide the visualization of rMATs output?
rMATs visualization
updated 23 months ago by ▴ 10 • written 4.2 years ago by ▴ 30
0
votes
0
replies
637
views
News: Become a Bioinformatics Pro: Easy Understanding Starts Here
Structural-Bioinformatics
updated 23 months ago by 45k • written 23 months ago by • 0
121,962 results • Page 194 of 2440
Recent Votes
A: Which is the proper RNA-seq count table transformation to perform hierarchial cl
Answer: Differences between published differential gene expression results and own analy
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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Comment: ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues usin by Ben • 0
write.table(df1, "df1.txt", sep = "\t", row.names = T, col.names = T, quote = FALSE)
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
That is good confirmation. Bacl to the error message. > I don't know how to fix this, given that I already did the trimming steps. DId yo…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
Honestly, those things shouldn't result in a considerable discrepancy. The largest difference will come from the post-processing & analysi…
Answer: Differences between published differential gene expression results and own analy by Ales ▴ 50
I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
Answer: Help interpreting BLASTn results and phylogenetic tree for genetics practical by Mensur Dlakic ★ 30k
I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
Answer: Differences between published differential gene expression results and own analy by yura.grabovska ▴ 830
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Comment: Functional prediction for proteins of bacteria. by colindaven 8.0k
Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
Comment: Errors with RSEM/bowtie2 by Olivia • 0
Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by Guilherme • 0
Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
Comment: help with modkit on nanopore sequencing data. by andres.firrincieli 3.9k
On the DMR tutorial page, they retrieve Human CpG Islands from the UCSC Table Browser. You can do the same thing for Mouse CpG Islands. Hav…
Comment: After doublet detection in 10x scRNA-Seq data, there is still evidence of double by yura.grabovska ▴ 830
Yes but the problem is that biological knowledge is never fully encompasing. While I can say that a cell expressing CD45 alongside astrocyt…
Comment: DNA copy number blacklist for excluding common unreliable regions by yura.grabovska ▴ 830
Human genome, ideally hg38
Comment: Is Newbler still available for download by anweshaash • 0
Hello, I am wondering if you got access to the software or not. I am looking to use Newbler for my research and I contacted Roche too but t…
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
> I have previously run Trinity with the Trimmomatic step as well as CD-HIT-EST. I assume you did the above to generate the transcriptome,…
Answer: With 10x Visum HD : How to map the barcode id to the barcode sequence ? by sacha ★ 2.5k
Got it https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-inclusion-list-formerly-barcode-whitelist
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