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6,956 results • Page 5 of 140
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12
votes
7
replies
6.4k
views
6 follow
Convert FPKM to TPM in R
r TPM normalization meta-analysis
updated 10 months ago by 44k • written 2.3 years ago by ▴ 170
12
votes
7
replies
2.0k
views
Shrink logFC values after edgeR
logFC edgeR
updated 10 months ago by ★ 7.8k • written 11 months ago by ▴ 10
12
votes
5
replies
847
views
Forum: Books and Blogs guiding the programming practice in bioinformatic research?
R Python Programming
5 months ago by JustinZhang ▴ 120
12
votes
26
replies
5.7k
views
CUT&Tag data processing: peak caller choice and typical peak size profile
CUTandTag MACS2 SEACR ChIPseq gopeaks
updated 12 weeks ago by ★ 18k • written 2.1 years ago by ▴ 50
12
votes
13
replies
7.0k
views
7 follow
Centrimo error: Template does not contain data section
ChIP-Seq MEME
updated 7 months ago by ▴ 70 • written 5.3 years ago by ▴ 70
12
votes
17
replies
7.2k
views
9 follow
ACMG assignment tools
wes acmg WES WGS
updated 9 months ago by • 0 • written 4.6 years ago by ▴ 190
12
votes
9
replies
687
views
7 follow
Best Approach to Identify Human-C. elegans Orthologs?
c.elegans Orthologs Homologs Genomics
6 weeks ago by bioinformatics_rk • 0
12
votes
3
replies
663
views
How to use GFF3 annotation to split genome fasta into gene sequence fasta in R
R GFF3 fasta genome
updated 5 months ago by 44k • written 5 months ago by ★ 1.3k
12
votes
6
replies
1.2k
views
Pangenome of plant
pangenome plant
9 months ago by analyst ▴ 50
12
votes
5
replies
2.7k
views
BD Rhapsody software - single cell seq
bd rhapsody single-cell
updated 11 days ago by 86k • written 20 months ago by 7.0k
12
votes
16
replies
12k
views
8 follow
fpkm to tpm conversion
R next-gen
updated 11 months ago by ★ 4.3k • written 7.3 years ago by ▴ 20
12
votes
14
replies
2.9k
views
8 follow
Forum: Recovering bam files after unknown deletion in the storage
photorec bam sequencing
written 5.6 years ago by ▴ 70
12
votes
13
replies
12k
views
11 follow
how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
rna-seq
updated 3 months ago by • 0 • written 7.2 years ago by ▴ 80
12
votes
12
replies
1.7k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 4 months ago by 44k • written 9 months ago by • 0
12
votes
2
replies
834
views
News: 8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop RNA-Seq DNA-Seq Illumina
9 months ago by David Langenberger 11k
12
votes
6
replies
1.2k
views
Downloading paired end fastq data from SRA
SRA single-cell RNA-Seq
4 months ago by Matheus • 0
12
votes
12
replies
1.7k
views
Processing fastq files for genome assembly
fastq vcf assembly amino-acid
updated 10 months ago by 20k • written 10 months ago by ▴ 20
12
votes
7
replies
16k
views
7 follow
How to download dbSNP153 vcf files in hg19/GRCH37 version
dbsnp153 vcf
updated 7 months ago by ▴ 260 • written 5.4 years ago by ★ 9.6k
12
votes
9
replies
7.9k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 9 months ago by 44k • written 4.9 years ago by ▴ 90
12
votes
5
replies
1.2k
views
Tutorial: removeBatchEffect explained using base R linear models
removebatcheffects limma batch-effect
updated 11 weeks ago by ▴ 70 • written 8 months ago by ▴ 420
12
votes
19
replies
15k
views
11 follow
SnpMatrix from VCF file
VCF Eqtl MatrixEQTL SnpMatrix vcftools
updated 10 months ago by ▴ 10 • written 7.9 years ago by ▴ 110
11
votes
22
replies
5.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 9 months ago by 44k • written 5.7 years ago by ▴ 280
11
votes
9
replies
13k
views
10 follow
Genome assembly statistical tools
Assembly statistics
updated 9 months ago by • 0 • written 5.4 years ago by ▴ 10
11
votes
12
replies
15k
views
11 follow
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
updated 10 months ago by ★ 2.1k • written 4.8 years ago by ▴ 60
11
votes
13
replies
14k
views
7 follow
log2 fold change in RNA-seq analysis
fold log2 change
updated 7 months ago by ▴ 10 • written 3.0 years ago by ▴ 10
11
votes
10
replies
10k
views
Duplicates In The Context Of Deep Sequencing
sequencing duplicates
updated 4 months ago by ▴ 10 • written 12.1 years ago by ★ 4.1k
11
votes
9
replies
3.1k
views
8 follow
Why it is not use UMIs for RNA-seq?
RNA-Seq UMIs scRNA-seq
updated 6 months ago by ▴ 30 • written 4.2 years ago by ★ 1.3k
11
votes
2
replies
697
views
Tutorial: Avoiding the Pitfalls of the Anaconda License: A Practical Guide
conda Anaconda license
10 weeks ago by Juke34 9.0k
11
votes
7
replies
501
views
6 follow
Forum: How people usually perform scRNA Seq Analysis on HPC?
hpc Single-cell cluster scRNA-Seq
updated 5 weeks ago by 44k • written 5 weeks ago by • 0
11
votes
4
replies
1.3k
views
Why employ normalization methods, and how can they be utilized in DEG analysis?
R DEGs normalization
10 months ago by wyt1995 ▴ 40
11
votes
1
reply
295
views
Cannot use more than 2 sample IDs when demultiplexing using Demuxlet
SNP variant demultiplexing Demuxlet scRNAseq
4 months ago by Chilly ★ 1.3k
11
votes
12
replies
1.6k
views
dedup STAR transcriptome file using umi_tools
rna-seq umi transcriptome umi_tools
10 weeks ago by ATRX ★ 1.1k
11
votes
12
replies
1.5k
views
Set the same Y scale for different plots
ggplot2 R
7 months ago by G.S ▴ 60
11
votes
6
replies
3.1k
views
Forum: Science Games For Citizen Science And Educational Purposes
education
written 12.0 years ago by 11k
11
votes
8
replies
5.9k
views
Multi-mapping High with featureCounts but not STAR
RNA-Seq sequencing alignment
updated 10 months ago by 148k • written 5.6 years ago by ▴ 70
11
votes
7
replies
3.6k
views
Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 9 months ago by ★ 2.8k • written 9 months ago by ▴ 10
11
votes
36
replies
6.7k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 9 months ago by 44k • written 6.4 years ago by ▴ 640
11
votes
18
replies
2.0k
views
6 follow
Interpreting phylogenetics tree
phylogenetic-tree itol phylogenetics
updated 6 weeks ago by ★ 1.6k • written 4 months ago by ▴ 50
11
votes
5
replies
732
views
Herald: The Biostar Herald for Monday, November 04, 2024
herald
updated 10 weeks ago by ★ 2.8k • written 10 weeks ago by 3.3k
11
votes
11
replies
992
views
Can't increase font size for x axis
R ggplot2
6 months ago by Chris ▴ 340
11
votes
17
replies
6.7k
views
6 follow
ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data)
RNA-Seq R ESTIMATE
updated 3 months ago by • 0 • written 4.4 years ago by ▴ 10
11
votes
6
replies
8.2k
views
Transposable Elements positions in genome (GTF file)
Transposable-elements genome annotation
updated 3 months ago by • 0 • written 9.8 years ago by ▴ 350
10
votes
12
replies
3.0k
views
How to download FASTQ files from the European Nucleotide Archive (ENA) to use them with FastQC etc..
ENA fastq R FastQC python
updated 7 months ago by ▴ 130 • written 14 months ago by ▴ 50
10
votes
5
replies
10k
views
What Is The Meaning Of Snp Strand
snp mapping strand
updated 7 months ago by ▴ 260 • written 13.4 years ago by ▴ 60
10
votes
10
replies
1.2k
views
Message seen when performing alignment
bwa alignment
updated 11 months ago by 148k • written 11 months ago by • 0
10
votes
8
replies
5.2k
views
7 follow
What is the best practice of scRNA workflow for multiple patients and samples using Seurat
scRNA sing-cell RNA seurat integrate
updated 8 weeks ago by ▴ 50 • written 4.2 years ago by ▴ 70
10
votes
10
replies
11k
views
9 follow
Free Virtual Ligand Screening Software
drug software
written 13.1 years ago by ★ 1.0k
10
votes
8
replies
5.9k
views
Different bigwig file sizes between BedgraphToBigwig and bamCoverage
ucsc bigwig BedgraphToBigWig bamCoverage deeptools
updated 7 months ago by ▴ 70 • written 6.4 years ago by ▴ 420
10
votes
16
replies
20k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 8 months ago by 165k • written 6.4 years ago by ▴ 180
10
votes
6
replies
940
views
6 follow
Slow BLAST speed when database on external drive?
BLAST
updated 11 months ago by 4.7k • written 11 months ago by ▴ 40
6,956 results • Page 5 of 140
Recent Votes
Comment: Strange offsetting in deeptools?
Answer: Strange offsetting in deeptools?
Comment: Strange offsetting in deeptools?
A: Counting base and nucleotide frequency of multifasta file
Step by step tutorial to replicate a genomics figure
Answer: b37 liftover
Comment: b37 liftover
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Scholar to rfran010 ★ 1.3k
Popular Question to heskett ▴ 110
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Recent Replies
Comment: Strange offsetting in deeptools? by Elijah ▴ 10
Oh I see! Yes, this is very clear, thank you so much for the in-depth answer :) I think what I was missing was exactly what you said - tha…
Comment: Strange offsetting in deeptools? by rfran010 ★ 1.3k
Yes, the mix up is maybe that your RNA can come from plus or minus strand. Depending on which strand the RNA originated from, Read1 will c…
Comment: Strange offsetting in deeptools? by Elijah ▴ 10
Thank you for your reply! Does filterRNAstrand not remove read 2? From the documentation for filterRNAstrand: "Selects RNA-seq reads (sin…
Comment: Issue with CIBERSORTx Error 139 by jared.andrews07 ★ 18k
I believe the site was down earlier today for a bit as well, so it may have been on their end. They have a banner saying user login is now …
Answer: b37 liftover by Giulio Genovese ▴ 590
Using [BCFtools/liftover](https://doi.org/10.1093/bioinformatics/btae038) will automatically take care of: - flexible contig names (e.g. …
Comment: circos ignoring the ticks and plots by GenoMax 148k
Please copy and paste the actual code instead of posting screenshots. You can format the text as `code` by using `101010` button in edit wi…
Answer: Strange offsetting in deeptools? by rfran010 ★ 1.3k
It does seem like you want to set offset as 1 to return the first base of your read. Have you done something to try and remove read2? T…
Comment: Merging gvcf files between Dragen and other calling tools by Pierre Lindenbaum 165k
those are GVCF files, not standard VCF files, you cannot merge those files without using the INFO column.
Comment: Merging gvcf files between Dragen and other calling tools by tacrolimus ▴ 140
Did you not merge them all then or just rid of the INFO entirely? Many thanks!
Comment: Merging gvcf files between Dragen and other calling tools by Pierre Lindenbaum 165k
Hi tried to use GATK CombineGVCFs a while ago, without success, the INFO are not compatible.
Comment: Issue with CIBERSORTx Error 139 by Hamdache • 0
Thanks for your help I will keep you updated
Comment: Download SRA raw data using efetch by biofysikos • 0
Thank you @genomax! It all makes sense (for now).
Comment: Issue with CIBERSORTx Error 139 by GenoMax 148k
If you are able to resolve the name of the resource by doing `host cibersortx.stanford.edu` then it is possible that the method/API you are…
Comment: Download SRA raw data using efetch by GenoMax 148k
> I can just use curl to download the URL extracted by efetch As long as you are aware of the limitations (e.g. there may be a single file…
Comment: Issue with CIBERSORTx Error 139 by Hamdache • 0
Apparently yes I tried ping -c 4 google.com ping -c 4 google.com PING google.com (142.251.37.174) 56(84) bytes of data. 64 by…
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