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683 results • Page 1 of 14
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54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 29 days ago by • 0 • written 12.1 years ago by ★ 2.9k
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 18 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 18 days ago by 19k • written 20 days ago by ▴ 580
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 1 day ago by ▴ 170 • written 7.1 years ago by ▴ 240
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 29 days ago by ▴ 10 • written 10.3 years ago by ▴ 180
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 15 days ago by • 0 • written 12.8 years ago by ★ 1.7k
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 29 days ago by 43k • written 4.6 years ago by ★ 1.4k
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 22 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 15 days ago by ▴ 10 • written 3.2 years ago by ▴ 120
14
votes
2
replies
7.1k
views
Trouble with Pilon installation
polishing pilon installation
updated 23 days ago by • 0 • written 7.3 years ago by ★ 1.4k
13
votes
14
replies
950
views
High Malat-1 expression in single cell data
single-cell
updated 10 days ago by ▴ 40 • written 19 days ago by ▴ 40
11
votes
12
replies
1.2k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 29 days ago by 43k • written 4 weeks ago by • 0
11
votes
3
replies
345
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 10 days ago by ▴ 200 • written 10 days ago by • 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 11 days ago by 161k • written 5.8 years ago by ▴ 180
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 22 days ago by ★ 5.1k • written 6.0 years ago by ▴ 520
10
votes
14
replies
790
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 11 days ago by 142k • written 17 days ago by • 0
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 29 days ago by 43k • written 4.6 years ago by ▴ 140
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 7 days ago by • 0 • written 5.7 years ago by ▴ 20
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 7 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 29 days ago by 43k • written 10.0 years ago by ▴ 250
8
votes
8
replies
764
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 23 days ago by 14k • written 24 days ago by ▴ 10
8
votes
5
replies
6.5k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 22 days ago by ★ 2.5k • written 10 weeks ago by • 0
7
votes
2
replies
330
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 24 days ago by ▴ 400 • written 26 days ago by • 0
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 23 days ago by ▴ 860 • written 6.2 years ago by ▴ 10
7
votes
6
replies
600
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
27 days ago by analyst ▴ 50
7
votes
16
replies
956
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
19 days ago by Ruqaiya • 0
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 6 days ago by • 0 • written 6.7 years ago by • 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 13 days ago by ▴ 10 • written 2.0 years ago by • 0
6
votes
7
replies
393
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 days ago by sansan_96 ▴ 90
6
votes
3
replies
230
views
Interpretting IGV output
IGV
updated 26 days ago by 8.7k • written 26 days ago by ▴ 50
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 7 days ago by • 0 • written 6.5 years ago by ▴ 130
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
3 days ago by Arton ▴ 10
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 29 days ago by 43k • written 5.0 years ago by ▴ 140
6
votes
4
replies
301
views
Details on salmon index
Salmon
updated 1 day ago by 6.6k • written 2 days ago by • 0
6
votes
2
replies
243
views
EdgeR - relationship between logFC and coefficients
differential-expression r edger
updated 8 days ago by ★ 7.2k • written 8 days ago by ▴ 10
5
votes
7
replies
498
views
RNA seq analysis
DESeq RNA-seq
3 days ago by Jacek ▴ 20
5
votes
4
replies
732
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
29 days ago by BioinfGuru ★ 1.7k
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 29 days ago by 43k • written 9.2 years ago by ▴ 110
5
votes
3
replies
758
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 29 days ago by • 0 • written 10 months ago by ▴ 310
5
votes
2
replies
439
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 22 days ago by ▴ 10 • written 3 months ago by ▴ 20
5
votes
3
replies
321
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 18 days ago by ★ 1.2k • written 18 days ago by • 0
5
votes
4
replies
720
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
24 days ago by kirillkirilenko ▴ 40
5
votes
5
replies
349
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 16 days ago by ▴ 40 • written 16 days ago by ▴ 150
5
votes
5
replies
323
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
10 days ago by Chris ▴ 280
5
votes
2
replies
350
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 19 days ago by 19k • written 22 days ago by ▴ 40
5
votes
6
replies
606
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 18 days ago by ▴ 760 • written 19 days ago by ▴ 40
4
votes
2
replies
270
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 13 days ago by 43k • written 15 days ago by ▴ 40
4
votes
2
replies
282
views
GRCh38.gmap file
gnomix gmap
13 days ago by lorena9132 ▴ 10
4
votes
8
replies
772
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 21 days ago by 35k • written 22 days ago by ▴ 10
683 results • Page 1 of 14
Recent Votes
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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