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1,000 results • Page 5 of 20
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2
votes
7
replies
890
views
Should we assume UMI-based scRNAseq data is not compositional?
compositional scRNAseq
9 months ago by cwwong13 ▴ 40
0
votes
7
replies
1.4k
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
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 11 months ago by 44k • written 8.1 years ago by ▴ 50
5
votes
7
replies
997
views
Salmon index not progressing
salmon
updated 8 months ago by 54k • written 8 months ago by ▴ 160
0
votes
7
replies
746
views
error MarkerScanner.pl
amphora2
updated 5 months ago by 44k • written 5 months ago by • 0
5
votes
7
replies
879
views
About the value in bigwig file
ATAC-seq
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 280
1
vote
7
replies
839
views
What could be the rage for Average Coverage after Assembly
viral-genome spades coverage de-novo-assembly
updated 10 months ago by 44k • written 10 months ago by ▴ 70
2
votes
7
replies
599
views
Need a link to OLDERADO server
pdb protein nmr structure
10 weeks ago by b2003 • 0
0
votes
7
replies
635
views
Trying to extract .cram file read sequences into array
CRAM pysam reads samtools
12 weeks ago by sacryt • 0
1
vote
7
replies
4.1k
views
Adjust width of annotations in pheatmap
R heatmap
updated 7 months ago by 88k • written 5.5 years ago by ▴ 30
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 10 months ago by 142k • written 10 months ago by • 0
0
votes
7
replies
2.7k
views
How to perform gene annotation in kallisto?
Gene kallisto annotation
updated 9 months ago by • 0 • written 2.7 years ago by ▴ 100
1
vote
7
replies
938
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 8 weeks ago by 44k • written 10 months ago by ▴ 100
0
votes
7
replies
947
views
SNPeff problem
snpEff
updated 10 months ago by 44k • written 10 months ago by • 0
2
votes
7
replies
977
views
Removing duplicates
duplicates ONT minimap2
updated 4 weeks ago by ▴ 590 • written 5 weeks ago by • 0
4
votes
7
replies
1.2k
views
Statistical test to compare data across timepoints
Statistics
updated 7 months ago by 4.6k • written 7 months ago by ▴ 20
2
votes
7
replies
686
views
Maker: Combining Annotations for Large Genomes
Maker Genome annotation
3 months ago by Kinoppy • 0
3
votes
7
replies
536
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
11 weeks ago by Fadlilah ▴ 10
3
votes
7
replies
1.4k
views
VG Giraffe multi-mapped reads and definition for MAPQ score
vg
9 months ago by Hendricks27 • 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
4
votes
7
replies
2.3k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 3 months ago by 44k • written 22 months ago by ▴ 10
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 44k • written 5.5 years ago by ★ 2.6k
2
votes
7
replies
728
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq contamination
updated 10 weeks ago by ▴ 410 • written 10 weeks ago by ▴ 20
3
votes
7
replies
3.3k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter vcftools sequencing
updated 11 months ago by 44k • written 4.2 years ago by ▴ 10
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
6
votes
7
replies
614
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 4 months ago by 54k • written 4 months ago by • 0
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 44k • written 4.9 years ago by ▴ 120
1
vote
7
replies
933
views
help with weird PCA? (vcfR)
vcftools vcfR R
6 months ago by MaeBH • 0
0
votes
7
replies
601
views
Iterate through Seurat object to add patient information
R Seurat
updated 3 months ago by 44k • written 3 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
1
vote
7
replies
1.3k
views
For loop STAR not working
RNA-Seq STAR
updated 11 months ago by 44k • written 2.9 years ago by ▴ 30
0
votes
7
replies
794
views
Search for specific SNPs in VCF files of patients.
ANNOVAR vcftools bcftools GATK VCF
updated 4 months ago by 44k • written 5 months ago by ▴ 10
0
votes
7
replies
969
views
For loop RNA Sequencing alignment
RNA STAR
updated 11 months ago by 44k • written 19 months ago by • 0
0
votes
7
replies
1.4k
views
fasterq-dump outputs "Cannot use '--ngc' as ngc file."
snakemake sra-tools SRA
updated 11 months ago by 44k • written 12 months ago by ▴ 80
1
vote
7
replies
1.6k
views
Typical percentage of multimapping reads in human rna-seq?
RNA-seq alignment Bowtie2 STAR
updated 11 months ago by 142k • written 11 months ago by ▴ 60
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 6 weeks ago by 44k • written 3.8 years ago by ▴ 20
0
votes
7
replies
942
views
Mugsy error -directory must be a directory
Mugsy
updated 8 months ago by 44k • written 3.5 years ago by ▴ 160
0
votes
7
replies
494
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap 1000Genome 1000G
updated 3 months ago by ▴ 410 • written 3 months ago by ▴ 210
0
votes
7
replies
1.2k
views
Tool-Compare Sequences within a Single Tree.
mutations sequence alignment
updated 11 months ago by 44k • written 5.2 years ago by • 0
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
0
votes
7
replies
1.2k
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 11 months ago by 4.2k • written 12 months ago by ▴ 40
2
votes
7
replies
1.3k
views
Weirdness in annotation (missing allele frequencies)
allele-frequency gnomad annovar
updated 7 months ago by 44k • written 8 months ago by • 0
0
votes
7
replies
3.9k
views
MUMmer plot visualization
MUMmer plot
updated 3 months ago by • 0 • written 3.3 years ago by ▴ 90
8
votes
7
replies
607
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 3 months ago by 44k • written 3 months ago by ▴ 100
2
votes
7
replies
547
views
How to predication/annotation trans-splicing in genome
trans-splicing genome annotation mitochondrial
3 months ago by oasiswho • 0
1
vote
7
replies
587
views
Question regarding WGCNA
WGCNA Network-construction
13 days ago by deepak • 0
1
vote
7
replies
961
views
Filtering a 10X generated .bam file based on a list of barcodes
snRNA-seq scRNA-seq samtools BAM RNA-seq
7 months ago by jhnicolas • 0
1
vote
7
replies
2.0k
views
Filtering a VCF by "IMP" flag in INFO with bcftools
vcf bcftools
updated 11 months ago by 44k • written 20 months ago by ▴ 40
0
votes
7
replies
941
views
Tool for Iterative mapping
read-mapping
updated 11 months ago by 44k • written 4.1 years ago by ▴ 10
0
votes
7
replies
672
views
Using Primer3 with python to genotype a SNP at a particular position
primer3 python position primer
updated 6 months ago by 162k • written 6 months ago by • 0
1,000 results • Page 5 of 20
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Classifying normal vs cancer tissues from mutational data
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Comment: FastQC interpretation - 16S sequencing
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Recent Replies
Comment: Trimmomatic running but files containing purged reads are empty by GenoMax 142k
> Why is trimmomatic not removing any reads? It is not mandatory that your data have extraneous/adapter sequence. If no extraneous sequenc…
Comment: FastQC interpretation - 16S sequencing by GenoMax 142k
Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
Comment: FastQC interpretation - 16S sequencing by Christopher • 0
@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
Comment: FastQC interpretation - 16S sequencing by GenoMax 142k
> My specific question is about the feasibility of per base sequence content analysis and whether I should be concerned about a particular …
Comment: How to get the ratio of allele counts from GATK derived VCF file? by anikcropscience ▴ 230
But I used the same bam files in both freebayes and GATK. Even the overlapping SNPs from both software are giving different estimates in te…
Comment: How to get the ratio of allele counts from GATK derived VCF file? by Pierre Lindenbaum 162k
may be downsampling(?), QC failing reads ?
Comment: How to get the ratio of allele counts from GATK derived VCF file? by anikcropscience ▴ 230
Thank you. However, I extracted the AD for each SNP that gives two numbers separated by a comma. I guess the first one is for reference and…
Answer: How to get the ratio of allele counts from GATK derived VCF file? by Pierre Lindenbaum 162k
> However, I am doing SNP calling using GATK, but there is no such information field for reference and alternate allele counts. it's in …
Comment: samtools write-index by GenoMax 142k
> The index file is older than the data file: alignment.sorted.bam.bai I don't think that warning is going to cause any issues. Not sure w…
Comment: samtools write-index by Pierre Lindenbaum 162k
can you please retry, but add rm -vf alignment.sorted.bam.bai before invoking minimap2. And `-o alignment.sorted.bam` should be enoug…
Answer: from CRAM to fastq by Pierre Lindenbaum 162k
if the CRAM/BAM is paire-end, it **must** be sorted on query name using samtools collate https://x.com/lh3lh3/status/1132756684789768202 …
Comment: from CRAM to fastq by machaalani29 • 0
one of the issues is that I am not very sure how the sequencing was done, but I think it was single end. any suggestions hoot do that?
Comment: from CRAM to fastq by machaalani29 • 0
the option -c is to compress the file
Comment: from CRAM to fastq by GenoMax 142k
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
Comment: converting transcript IDs (Ensembl) to gene symbols in R by GenoMax 142k
https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
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