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1,000 results • Page 5 of 20
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1
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7
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828
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What could be the rage for Average Coverage after Assembly
viral-genome spades coverage de-novo-assembly
updated 10 months ago by 43k • written 10 months ago by ▴ 70
4
votes
7
replies
792
views
Alternative for grep in a for loop
linux
updated 7 months ago by 43k • written 7 months ago by ▴ 20
2
votes
7
replies
1.1k
views
error: BLAST database name is missing. Please edit provean.sh file to add the name.
provean error
updated 8 months ago by 142k • written 8 months ago by • 0
0
votes
7
replies
1.0k
views
All question mark quality scores on several studies
quality-score shotgun illumina
updated 11 months ago by 43k • written 11 months ago by ▴ 10
4
votes
7
replies
1.1k
views
Statistical test to compare data across timepoints
Statistics
updated 7 months ago by 4.6k • written 7 months ago by ▴ 20
0
votes
7
replies
1.4k
views
fasterq-dump outputs "Cannot use '--ngc' as ngc file."
snakemake sra-tools SRA
updated 10 months ago by 43k • written 12 months ago by ▴ 80
3
votes
7
replies
392
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
16 days ago by salias • 0
3
votes
7
replies
3.3k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter vcftools sequencing
updated 10 months ago by 43k • written 4.2 years ago by ▴ 10
0
votes
7
replies
583
views
Iterate through Seurat object to add patient information
R Seurat
updated 3 months ago by 43k • written 3 months ago by ▴ 100
1
vote
7
replies
947
views
Filtering a 10X generated .bam file based on a list of barcodes
snRNA-seq scRNA-seq samtools BAM RNA-seq
6 months ago by jhnicolas • 0
5
votes
7
replies
974
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq sequencing
updated 12 months ago by • 0 • written 4.4 years ago by ▴ 50
3
votes
7
replies
1.4k
views
Find 3'UTRs for species
Assembly alignment
updated 11 months ago by 43k • written 4.7 years ago by ▴ 110
1
vote
7
replies
917
views
help with weird PCA? (vcfR)
vcftools vcfR R
6 months ago by MaeBH • 0
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 28 days ago by 43k • written 7.7 years ago by ▴ 70
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools RNA-seq NGS
updated 8 months ago by 43k • written 5.8 years ago by ▴ 40
0
votes
7
replies
2.2k
views
Command not found after pip install spliceai
software error
updated 7 months ago by • 0 • written 3.5 years ago by • 0
0
votes
7
replies
1.3k
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 7 months ago by ▴ 900 • written 8 months ago by ▴ 20
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 8 months ago by 43k • written 4.2 years ago by ▴ 70
2
votes
7
replies
4.7k
views
SRA toolkit internet settings
sratoolkit fastq-dump sequencing RNA-Seq
updated 10 months ago by 43k • written 7.8 years ago by ▴ 90
4
votes
7
replies
823
views
Help with weighted nearest neighbor analysis
seurat single-cell
8 months ago by Chris ▴ 280
0
votes
7
replies
549
views
SNP calling with many samples using bcftools
bcftools SNP multithreading
6 months ago by George ▴ 10
0
votes
7
replies
473
views
Error "ckalloc: request for negative space" about multiz
multiz
10 weeks ago by marh32 • 0
1
vote
7
replies
1.6k
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto STAR RNA-seq Transcript_variants
12 months ago by sohail.mbio • 0
3
votes
7
replies
1.4k
views
VG Giraffe multi-mapped reads and definition for MAPQ score
vg
9 months ago by Hendricks27 • 0
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT TF-footprinting ATAC-seq
updated 11 months ago by 43k • written 5.5 years ago by ★ 2.6k
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 7 months ago by 100k • written 5.9 years ago by ▴ 10
2
votes
7
replies
1.8k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence ncbi gene genbank
updated 11 months ago by 43k • written 6.2 years ago by ▴ 70
0
votes
7
replies
624
views
Trying to extract .cram file read sequences into array
CRAM pysam reads samtools
11 weeks ago by sacryt • 0
0
votes
7
replies
475
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap 1000Genome 1000G
updated 3 months ago by ▴ 400 • written 3 months ago by ▴ 210
2
votes
7
replies
536
views
How to predication/annotation trans-splicing in genome
trans-splicing genome annotation mitochondrial
3 months ago by oasiswho • 0
0
votes
7
replies
467
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 7 weeks ago by 142k • written 7 weeks ago by • 0
6
votes
7
replies
598
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 4 months ago by 54k • written 4 months ago by • 0
3
votes
7
replies
1.1k
views
Use giraffe in vg
giraffe vg
updated 10 months ago by ▴ 460 • written 10 months ago by • 0
0
votes
7
replies
959
views
For loop RNA Sequencing alignment
RNA STAR
updated 10 months ago by 43k • written 19 months ago by • 0
0
votes
7
replies
2.7k
views
How to perform gene annotation in kallisto?
Gene kallisto annotation
updated 8 months ago by • 0 • written 2.7 years ago by ▴ 100
1
vote
7
replies
531
views
Question regarding WGCNA
WGCNA Network-construction
6 days ago by deepak • 0
4
votes
7
replies
842
views
SNP IDs
SNP
6 months ago by kl ▴ 10
1
vote
7
replies
1.3k
views
For loop STAR not working
RNA-Seq STAR
updated 10 months ago by 43k • written 2.9 years ago by ▴ 30
1
vote
7
replies
1.9k
views
Filtering a VCF by "IMP" flag in INFO with bcftools
vcf bcftools
updated 11 months ago by 43k • written 19 months ago by ▴ 40
1
vote
7
replies
1.9k
views
for loop in a bash script
bash
updated 10 months ago by 43k • written 2.6 years ago by • 0
1
vote
7
replies
1.6k
views
Typical percentage of multimapping reads in human rna-seq?
RNA-seq alignment Bowtie2 STAR
updated 10 months ago by 142k • written 10 months ago by ▴ 60
0
votes
7
replies
7.3k
views
Problem in in alignment by muscle
sequence muscle alignment
updated 10 months ago by 43k • written 6.8 years ago by ▴ 70
0
votes
7
replies
4.5k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq alignment software-error next-gen sequence
updated 5 months ago by 43k • written 6.0 years ago by • 0
0
votes
7
replies
1.6k
views
Comparing the GVF file & VCF file
gvf dna vcf ensembl ngs
updated 6 months ago by • 0 • written 16 months ago by ▴ 30
1
vote
7
replies
926
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 7 weeks ago by 43k • written 9 months ago by ▴ 100
2
votes
7
replies
1.4k
views
VG mapping paired-end reads: error [xg]: multiple hits for XXX
variation-graph reads pangenome vg paired-end
8 months ago by nkls063408 • 0
7
votes
7
replies
618
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
3 months ago by Shane ▴ 20
3
votes
7
replies
2.6k
views
6 follow
Online BLAST search using R
BLAST R
updated 3 months ago by ▴ 140 • written 2.8 years ago by ▴ 20
4
votes
7
replies
1.5k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 142k • written 9 months ago by • 0
1,000 results • Page 5 of 20
Recent Votes
A: ensembl gene id
A: How to deal with the case that one gene symbol matches multiple ensembl ids?
Answer: DESeq2 error
Answer: Using ggplotly in R
Comment: How to calculate coverage of Nanopore long read data?
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
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Recent Replies
Comment: Sequencing Depth (Read Depth) Calculations by LucisTheFather • 0
Understood! Gonna try those two!
Comment: Sequencing Depth (Read Depth) Calculations by LucisTheFather • 0
Thank u very much!
Comment: How to extract cells of different species after mapping with combined genome? by GenoMax 142k
You have used the tag `snRNAseq`. I am not familiar with singleron tech but if you have sequence data you may be able to use `xenome` or `b…
Comment: bbmerge (bbmap) ~ error with insert size file output by GenoMax 142k
It may be best to go back to the original data and then do `bbmerge.sh` on it to get original insert size estimates (before any operations …
Comment: bbmerge (bbmap) ~ error with insert size file output by chrisk • 0
Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
Comment: bbmerge (bbmap) ~ error with insert size file output by chrisk • 0
Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
Comment: Inquiry about deseq2 transformation by Chen • 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output by Brian Bushnell 20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools by kl ▴ 10
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results by Arton ▴ 10
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Answer: Calculate allelic frequency from VEP output vcf file by ramiro.barrantes • 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation by Ram 43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas by Ash ▴ 10
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
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