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121,967 results • Page 220 of 2440
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5
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2
replies
1.4k
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Cell Barcode Identification and Counting
Cell-Barcoding
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 50
0
votes
5
replies
1.9k
views
CNA score calculation per cell
scRNA CNA
updated 2.1 years ago by ★ 19k • written 2.1 years ago by ▴ 40
0
votes
2
replies
1.9k
views
How to get the species abundance in metagenomic data sequenced by PacBio/Nanopore?
metagenome metagenomic pacbio nanopore
updated 2.1 years ago by 8.0k • written 4.9 years ago by • 0
1
vote
6
replies
2.2k
views
How are duplicated genes named under GTF file?
RNA-seq
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by ▴ 10
1
vote
6
replies
2.5k
views
Extract the true single-cell RNA sequencing reads for running SAHMI
scRNA
2.1 years ago by 573704669 • 0
0
votes
4
replies
1.6k
views
Kraken2 nucleotide custom database
ncbi kraken2 metagenomics
2.1 years ago by Natalia • 0
6
votes
8
replies
2.3k
views
Perbase base-depth
simple-depth base-depth perbase
2.1 years ago by S.O.T.AL-HASHIMI2 ▴ 60
0
votes
2
replies
1.1k
views
How to build a tree from SAM files?
SAM phylogeny alignment
2.1 years ago by Alina • 0
1
vote
2
replies
957
views
Detecting CNV's (copy number variation) in haploid yeast cells
CNV SV mapping Deep-sequencing
2.1 years ago by Rezenman • 0
0
votes
1
reply
1.2k
views
Converting gene id to entrez id with clusterprofiler
msu7 clusterProfiler annotationhub oryza_sativa
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
1
vote
1
reply
1.3k
views
Can you convert ASCII text to fastq?
ASCII fastq text
updated 2.1 years ago by ★ 1.2k • written 2.1 years ago by ▴ 10
2
votes
2
replies
1.2k
views
order of legend in ggscatter
ggscatter R
updated 2.1 years ago by 12k • written 2.1 years ago by ▴ 30
1
vote
2
replies
1.1k
views
BAM 2 FASTQ using Picard and Samtools
PAIREDENDFASTQ RNASequencing BAM SINGLETONS
2.1 years ago by kcarey • 0
0
votes
1
reply
1.2k
views
ModuleNotFoundError: No module named 'readfq' arises during the execution of kmergenie
kmergenie
updated 2.1 years ago by 89k • written 2.1 years ago by • 0
0
votes
2
replies
960
views
Extracting RNA sequence - single cell
Single-Cell
2.1 years ago by Skamboj • 0
2
votes
3
replies
1.3k
views
how to check if DE genes are enriched in custom genomic regions derived from epigenetic data
statistics multiomics epigenetics
2.1 years ago by Al • 0
1
vote
3
replies
1.9k
views
bcftoold guess ploidy
bcftools guess-ploidy
updated 2.1 years ago by ★ 3.1k • written 2.1 years ago by ▴ 230
0
votes
2
replies
846
views
Single Cell Data Analysis
Single-Cell
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
3
votes
1
reply
1.3k
views
R package to link NCBI taxonomy ID to bacterial properties (Gram stain, aerobe/anaerobe, etc)
R NCBI bacteria taxonomy
updated 2.1 years ago by 8.9k • written 2.2 years ago by ★ 2.1k
0
votes
1
reply
978
views
Gene set enrichment analysis / Kegg analysis
kegg DGE RNAseq GSEA DESeq2
updated 2.1 years ago by ▴ 110 • written 2.1 years ago by • 0
1
vote
2
replies
771
views
Pindel Error: I cannot find the file in configuration file
bam pindel
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 10
0
votes
4
replies
1.7k
views
error while installing peertools
peertools
updated 2.1 years ago by ★ 30k • written 3.9 years ago by ▴ 150
0
votes
0
replies
600
views
DCMS and stat_to_pvalue errors
Minotaur DCMS stat_to_pvalue
2.1 years ago by phudrux • 0
7
votes
9
replies
3.0k
views
6 follow
How can I transfer gene models to a new assembly?
gene Assembly
updated 2.2 years ago by 8.9k • written 5.5 years ago by ▴ 750
0
votes
2
replies
1.7k
views
Does STAR aligner use the maximum memory available?
STAR
updated 2.2 years ago by ★ 3.9k • written 2.2 years ago by • 0
5
votes
9
replies
2.5k
views
Is there a way to merge VCF indices?
vcf
updated 2.1 years ago by 45k • written 3.2 years ago by ▴ 70
33
votes
7
replies
28k
views
6 follow
VCF merge or concatenate?
snp VCF VCFTools
written 6.2 years ago by ▴ 80
0
votes
3
replies
1.6k
views
SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
SingleM SRAtoolkit
updated 2.2 years ago by ★ 2.1k • written 3.3 years ago by • 0
3
votes
3
replies
1.4k
views
How can I figure out where a mouse (C57BL/6J) genome is heterozygous?
mice SNP vcf
updated 2.2 years ago by ★ 2.1k • written 2.2 years ago by • 0
0
votes
0
replies
861
views
How to access the IT15/HTT gene fasta format of each sequenced individual from Phase 3 of the 1000 Genomes Project?
1000genomes fasta
updated 2.1 years ago by 45k • written 2.2 years ago by • 0
2
votes
4
replies
1.3k
views
Chip-Seq and DeepTools
Chip-Seq DeepTools
updated 2.2 years ago by ★ 3.1k • written 2.2 years ago by ▴ 40
0
votes
1
reply
1.2k
views
Stacks' populations.sumstats.tsv : interpreting pi for populations with one individual
summary-statistics Stacks pi
updated 2.2 years ago by 45k • written 2.2 years ago by • 0
3
votes
3
replies
1.5k
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 2.2 years ago by 3.9k • written 2.2 years ago by ▴ 750
1
vote
0
replies
674
views
News: Generalized Additive Models in R
R GAMs Courses
2.2 years ago by Physalia-courses ★ 2.6k
0
votes
2
replies
980
views
Help with an error with Homer
Homer
2.1 years ago by Chris ▴ 360
2
votes
4
replies
2.0k
views
How to get a list of gene names from macs2 peaks
chip-seq macs2 peaks
updated 2.2 years ago by 45k • written 2.2 years ago by ▴ 40
8
votes
4
replies
1.7k
views
LogFc vs t_statistic to estimate over/under expressed genes?
T-Test Limma DGE Voom
updated 2.2 years ago by 89k • written 2.2 years ago by ▴ 110
0
votes
0
replies
421
views
Merging biological replicated SNP data to create a consensus SNP data for a sample
SNP
updated 2.2 years ago by 45k • written 2.2 years ago by • 0
0
votes
2
replies
949
views
Plotting multiple sequence alignments from tblastn
tblastn visualization blast msa
2.2 years ago by dec986 ▴ 380
3
votes
3
replies
2.3k
views
How to get normalized counts corrected for variables in the design matrix of DESeq2 as an input for WGCNA
WGCNA vst DESeq2
2.1 years ago by Sara ▴ 40
6
votes
4
replies
4.0k
views
What are bitsets in Samtools flagstat output?
samtools nanopore mapping
2.1 years ago by kenneditodd ▴ 50
22
votes
15
replies
13k
views
12 follow
Alternatives To Liftover
liftover genome mapping
updated 16 months ago by • 0 • written 13.9 years ago by ▴ 170
1
vote
1
reply
900
views
Functional annotation of BRAKER output
BRAKER functional MAKER annotation
updated 2.2 years ago by 154k • written 2.2 years ago by • 0
3
votes
2
replies
3.1k
views
The result of Illumina/hap.py using the same file.
hap.py genome
updated 2.2 years ago by ▴ 530 • written 4.8 years ago by ▴ 30
0
votes
6
replies
2.2k
views
Somatic CNVs insilico evaluation
cnv wes
2.2 years ago by s.awasthy ▴ 30
0
votes
1
reply
805
views
How to construct a pan-genome graph using vg to create a GFA graph with "W" lines
vg
updated 2.2 years ago by 8.0k • written 2.2 years ago by • 0
0
votes
1
reply
2.5k
views
combine CNV calls from different softwares
R-Gada CNV PennCNV QuantiSNP
updated 2.2 years ago by ▴ 30 • written 8.3 years ago by ▴ 30
0
votes
3
replies
3.7k
views
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
R next-gen-sequencing absolute
updated 18 months ago by 45k • written 8.2 years ago by • 0
2
votes
7
replies
2.6k
views
Tool to search for missing genes among genome annotation versions?
annotation
updated 2.1 years ago by 4.8k • written 2.2 years ago by ▴ 250
0
votes
0
replies
594
views
Statistically Comparing Two DiffEx Gene Sets To Discern Treatment Effect
statistics expression design rnaseq ngs
2.2 years ago by James • 0
121,967 results • Page 220 of 2440
Recent Votes
Answer: How to create a consensus of a contig with samtools or bbmap?
Comment: Getting just fastqc.zip file?
alternate allele frequency and minor allele frequency
Calculating minor allele frequency for GnomAD VCF file
Hiring FT Remote Nextflow engineer to build ML workflows for cancer genomics
Answer: Gene expression equivalent of polygenic risk score ?
A: TRF output to .gff file
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Answer: How to convert gff to Sequin format? by GenoMax 154k
> $ gff3-to-tbl .../pharokka.gff .../Annotation/pharokka_cds_final_merged_output.tsv .../Consensus/reference.fasta .../Annotation/phanotate…
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
> Could this be an issue caused by the sequencing facility or just that they are in fact out of sync? We have no way to know. Did the sequ…
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Have included the links to the papers I mentioned in another comment for reference!
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
These are the 2 papers I mentioned previously that used data other than raw counts for their analysis: https://onlinelibrary.wiley.com/doi/…
Comment: Collect COV file by BedCoverage by eshrakaali_p • 0
Hello German , I am using clinCNV for WES and i faced the same error and this part of the error [1] "ERROR: your file with normal cove…
Comment: How to create a consensus of a contig with samtools or bbmap? by marongiu.luigi ▴ 760
sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
Comment: Help with Ideathon by V K • 0
Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap? by lieven.sterck 16k
You assembled a genome using samtools ???? that sounds very weird, if not impossible ... The header (SQ lines) is missing from your file b…
Answer: gnomad par region variants by benformatics 4.2k
The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon by Mensur Dlakic ★ 30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy by ATpoint 89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform) by rfran010 ★ 1.6k
Is it the version number in your data? e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ? by Picasa ▴ 690
Thanks a lot for your answer. I will check the paper.
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