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851 results • Page 4 of 18
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0
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7
replies
424
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Issues while running htseq-count
Candida-glabrata RNA-seq htseq-count
4 days ago by Foad ▴ 10
0
votes
7
replies
425
views
Using Primer3 with python to genotype a SNP at a particular position
primer3 python position primer
updated 15 days ago by 158k • written 15 days ago by • 0
0
votes
7
replies
529
views
Issue with Merging BCF Files: Invalid INFO id Error
bcftools
updated 11 days ago by 41k • written 13 days ago by • 0
8
votes
7
replies
9.4k
views
How to get just protein_coding genes using biomart in R
R sequencing rna-seq
updated 28 days ago by • 0 • written 8.0 years ago by ▴ 650
0
votes
7
replies
1.2k
views
Comparing the GVF file & VCF file
gvf dna vcf ensembl ngs
updated 15 days ago by • 0 • written 10 months ago by ▴ 30
7
votes
7
replies
541
views
RNA-Seq: Comparing Expression between Cancer Grades
factors rna-seq grades transcriptomics
27 days ago by foejvs546 ▴ 10
7
votes
7
replies
3.5k
views
Gap Alignment For Color Space Data (Blat For Color Space!)
blat short aligner solid
updated 18 days ago by 41k • written 13.6 years ago by ▴ 20
1
vote
7
replies
518
views
Adding median to Violin Plots ggplot2
seurat ViolinPlots ggplot2
updated 23 days ago by 41k • written 24 days ago by ▴ 40
13
votes
7
replies
6.0k
views
Go Functional Annotation
gene software
updated 21 days ago by 41k • written 13.6 years ago by ▴ 100
17
votes
7
replies
4.0k
views
How Difficult/Reliable Is It To Programmatically (Python) Look Up And Download Papers?
literature python text
updated 24 days ago by 41k • written 13.7 years ago by ▴ 270
2
votes
7
replies
13k
views
How too choose outgroup for rooting a phylogenetic tree?
phylogeny sequence alignment
updated 9 days ago by ▴ 30 • written 8.6 years ago by ★ 2.8k
1
vote
7
replies
374
views
featureCounts results: low rate of 'Successfully assigned alignments'
FeatureCounts HISAT2 RNA-seq
2 days ago by Hamtaro ▴ 10
0
votes
7
replies
1.5k
views
CIBERSORTx error: 'x' must be an array of at least two dimensions
matrix CIBERSORTx signature
updated 15 days ago by • 0 • written 17 months ago by • 0
4
votes
7
replies
628
views
Can clumpify.sh be used in a streaming fashion downstream of bcl-convert
bbmap clumpify bclconvert
updated 21 days ago by 19k • written 25 days ago by ▴ 20
2
votes
6
replies
386
views
how to merge multiple files based on column header
R statistics biostatistics
updated 28 days ago by 6.1k • written 29 days ago by ▴ 440
30
votes
6
replies
13k
views
What Are Some Good Free Bioinformatics And Computational Biology Books?
books online
updated 18 days ago by 41k • written 13.6 years ago by ★ 1.0k
11
votes
6
replies
691
views
6 follow
UMAP or TSNE for single cells?
single-cell
updated 8 days ago by ▴ 40 • written 15 days ago by ▴ 80
7
votes
6
replies
1.1k
views
How does 10x Genomics 3' single cell data have reads aligning to exons that aren't terminal?
single-nucleus rna-seq igv single-cell
updated 11 days ago by 41k • written 8 months ago by ▴ 40
8
votes
6
replies
476
views
Microarray data analysis with and without contrast
microarray limma
25 days ago by 1769mkc ★ 1.1k
0
votes
6
replies
1.6k
views
DiffBind dba.analyze never finishes
ChIP-Seq R DiffBind FAIRE-seq DESeq2
updated 14 days ago by ★ 2.0k • written 2.9 years ago by • 0
4
votes
6
replies
2.9k
views
Gene Similarity Search
conservation similarity
updated 18 days ago by 41k • written 13.6 years ago by ▴ 790
6
votes
6
replies
427
views
6 follow
How to align a genome fasta file from NCBI to a reference genome?
genome genetics alignment
updated 9 days ago by ★ 5.1k • written 10 days ago by • 0
2
votes
6
replies
2.1k
views
No best K value found
Assembly Kmergenie
updated 7 days ago by • 0 • written 6.8 years ago by ▴ 80
0
votes
6
replies
295
views
I made an error when using metawrap to binning
metagenome binning metawrap
4 days ago by alice005201314 • 0
2
votes
6
replies
463
views
Burrows-Wheeler transform
Python BWT DNA
updated 18 days ago by 41k • written 19 days ago by • 0
13
votes
6
replies
9.1k
views
What To Do With An Error In The Fastq Illumina Quality Scores
fastx-toolkit next-gen-sequencing fastq
updated 18 days ago by 41k • written 13.6 years ago by ★ 1.3k
0
votes
6
replies
498
views
Calculating ROC50 in R
ROC Protein R Homology
29 days ago by siu ▴ 150
4
votes
6
replies
6.0k
views
Single cell clutering after regressing out cell cycle effect using seurat
seurat scRNA-seq clustering
updated 24 days ago by ▴ 490 • written 4.2 years ago by ▴ 700
1
vote
6
replies
436
views
Read multiple vcf files into R
R vcf
26 days ago by sousapaulo16 • 0
2
votes
6
replies
680
views
need interpretations for the vg call output
vcf vg
13 days ago by Maxine ▴ 40
2
votes
6
replies
492
views
Annotating genome based on Sequence
genome annotation
updated 23 days ago by 4.5k • written 4 weeks ago by ▴ 10
4
votes
6
replies
392
views
Unexpected separation of RNA-seq samples on PCA plot
depletion PCA rRNA plot RNA-seq
11 days ago by Tihana ▴ 10
1
vote
6
replies
354
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
3 days ago by CTLong ▴ 20
0
votes
6
replies
512
views
Problem aligning target capture sequencing of a few hundred regions to the human reference genome
GATK4 bwa-mem target-capture-sequencing alignment
9 days ago by Miguel • 0
2
votes
6
replies
388
views
Quality filtering prior to pseudoalignment
fastp rna-seq pseudoalignment kallisto
updated 16 days ago by 19k • written 16 days ago by ▴ 20
13
votes
6
replies
352
views
6 follow
how to sort fasta file according to a header file
fasta
updated 10 days ago by 41k • written 10 days ago by ▴ 20
4
votes
6
replies
377
views
bwa mem hangs after a few thousand reads
bwa-mem alignment bwa calling variant
2 days ago by cee28 ▴ 30
5
votes
6
replies
3.8k
views
Accessing Cyanobase With The Biomart / Getbm Method
biomart r
updated 24 days ago by 41k • written 13.7 years ago by ▴ 790
4
votes
6
replies
543
views
Handling multiple fastq files per sample, per lane, per read out of the Cellranger bam to fastq workflow
bamtofastq cellranger RNA-seq
15 days ago by Erfanesi • 0
5
votes
6
replies
401
views
Generate Read counts from bam file
RNAseq reference_genome Deseq2 read_counts
updated 2 days ago by • 0 • written 3 days ago by • 0
2
votes
6
replies
490
views
Genotypes in vcf files
genotypes vcf
updated 7 days ago by 22k • written 7 days ago by ▴ 160
2
votes
6
replies
440
views
Filter a BED file based on genome coordinates for gene names
BED GTF GFF
updated 18 days ago by 41k • written 18 days ago by • 0
0
votes
6
replies
538
views
Help locating TCGA data from cbioportal
cancer TCGA RNA cbioportal CNA
17 days ago by ConvolutedGenome ▴ 20
0
votes
6
replies
549
views
Add braces to the DNA sequence for re quested primer position.
python subprocess
updated 16 days ago by 41k • written 22 days ago by • 0
4
votes
6
replies
560
views
BLAST hits on viruses relate to different host than used
Phage BLAST Metagenomics
6 days ago by DonPhager • 0
1
vote
6
replies
521
views
frequency plot for peaks
chip-seq chipseeker
updated 3 days ago by ▴ 400 • written 18 days ago by ▴ 10
3
votes
6
replies
420
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq cells mRNA expression gene
updated 15 hours ago by ★ 1.2k • written 2 days ago by ▴ 40
3
votes
6
replies
430
views
how extract information from the output text file?
R linux
22 days ago by satva72 • 0
0
votes
6
replies
375
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq Nanopore ONT differential expression
2 days ago by tw_140 • 0
2
votes
6
replies
6.9k
views
Extracting chimeric reads from mapping
RNA-Seq alignment samtools bwa
updated 2 days ago by • 0 • written 6.2 years ago by ▴ 20
851 results • Page 4 of 18
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Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated? by swbarnes2 13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by fluke • 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts by Istvan Albert 99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by beausoleilmo ▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by CTLong ▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC by ayasu • 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts by Brian Bushnell 19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by Brian Bushnell 19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters? by AMARU • 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
Comment: "MethylKit" package for WGBS data by viveksomya123 • 0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
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