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928 results • Page 1 of 19
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87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 21 days ago by • 0 • written 3.6 years ago by 3.2k
76
votes
72
replies
20k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
14 days ago by Kevin Blighe 87k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 21 days ago by • 0 • written 12.1 years ago by ★ 2.9k
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 10 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
38
votes
24
replies
2.0k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 9 days ago by 19k • written 12 days ago by ▴ 580
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 29 days ago by ▴ 60 • written 2.9 years ago by ★ 1.0k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 20 days ago by ▴ 10 • written 10.2 years ago by ▴ 180
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 24 days ago by 43k • written 4.0 years ago by ▴ 330
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 7 days ago by • 0 • written 12.8 years ago by ★ 1.7k
25
votes
11
replies
3.8k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 16 days ago by 43k • written 14.6 years ago by 100k
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 22 days ago by 43k • written 5.3 years ago by ▴ 130
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf fasta homopolymer repeat
updated 23 days ago by 43k • written 5.0 years ago by 47k
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 21 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 13 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 6 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
15
votes
6
replies
1.3k
views
6 follow
VCF to human friendly form?
vcf visualization
updated 24 days ago by 161k • written 20 months ago by ▴ 10
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing pilon installation
updated 15 days ago by • 0 • written 7.3 years ago by ★ 1.4k
13
votes
14
replies
803
views
High Malat-1 expression in single cell data
single-cell
updated 1 day ago by ▴ 40 • written 10 days ago by ▴ 40
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 22 days ago by 43k • written 6.8 years ago by ★ 1.3k
12
votes
2
replies
492
views
News: 8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop RNA-Seq DNA-Seq Illumina
29 days ago by David Langenberger 11k
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly statistics
updated 26 days ago by • 0 • written 4.8 years ago by ▴ 10
11
votes
9
replies
7.0k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 22 days ago by 43k • written 4.2 years ago by ▴ 80
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 21 days ago by 43k • written 21 days ago by • 0
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 21 days ago by 6.4k • written 10.9 years ago by ▴ 10
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 23 days ago by • 0 • written 9.3 years ago by ▴ 970
10
votes
14
replies
656
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 2 days ago by 142k • written 8 days ago by • 0
10
votes
6
replies
10.0k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 13 days ago by ★ 5.1k • written 6.0 years ago by ▴ 510
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 29 days ago by • 0 • written 8.8 years ago by ▴ 170
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 2 days ago by 161k • written 5.7 years ago by ▴ 180
10
votes
3
replies
276
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 1 day ago by ▴ 180 • written 2 days ago by • 0
10
votes
36
replies
5.9k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 22 days ago by 43k • written 5.7 years ago by ▴ 620
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 22 days ago by 43k • written 5.0 years ago by ▴ 330
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 22 days ago by 43k • written 7.4 years ago by ▴ 30
9
votes
4
replies
2.0k
views
Integration of RNA-Seq data with microarray data
microarray RNA-Seq batch-effect R
updated 22 days ago by 43k • written 4.0 years ago by ▴ 30
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 21 days ago by 43k • written 4.6 years ago by ▴ 140
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 21 days ago by 43k • written 10.0 years ago by ▴ 250
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 22 days ago by 3.0k • written 2.0 years ago by ▴ 230
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 13 days ago by ★ 2.4k • written 9 weeks ago by • 0
8
votes
5
replies
1.3k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 24 days ago by ▴ 210 • written 16 months ago by ★ 1.4k
8
votes
5
replies
6.2k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
8
votes
8
replies
717
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 14 days ago by 14k • written 15 days ago by ▴ 10
8
votes
10
replies
785
views
bash script
whole-genome-sequencing
updated 24 days ago by 43k • written 4 weeks ago by ▴ 30
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
22 days ago by Ram 43k
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 22 days ago by 43k • written 5.1 years ago by ▴ 100
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 14 days ago by ▴ 850 • written 6.2 years ago by ▴ 10
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 23 days ago by • 0 • written 6 months ago by ▴ 50
7
votes
7
replies
1.7k
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 24 days ago by ★ 2.5k • written 24 days ago by • 0
7
votes
1
reply
153
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 2 days ago by 14k • written 2 days ago by ▴ 360
7
votes
6
replies
556
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
18 days ago by analyst ▴ 50
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 20 days ago by 6.4k • written 16 months ago by ▴ 130
928 results • Page 1 of 19
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Answer: Which trajectory method is better !?
Answer: InferCNV results interpretation
Comment: absolute path for symbolic links in Snakefile
Deeptools computematrix of scale region give different result from ref point TSS.
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
cellranger error message
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Recent Replies
Comment: absolute path for symbolic links in Snakefile by Jesse ▴ 770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API by GenoMax 142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length by marco.barr ▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length by Pierre Lindenbaum 161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length by marco.barr ▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length by marco.barr ▴ 100
I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message by Max • 0
I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error: Log message: Requested sample(s…
Comment: Different output for read length by marco.barr ▴ 100
Thanks so much GenoMax, I'm sharing the link as you told me
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add a link here or you could a GitHub gist. You were suspended by biostars SPAM bot since you pasted link…
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add the link here. You were suspended by biostars SPAM bot since you pasted these links in quick successi…
Comment: RNA seq analysis by s.ghazala • 0
Could you clarify on what exactly you are referring to with "SRA data table". If you are retrieving fastq files (raw data), then you could …
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 100
Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS by tim.booth ▴ 60
Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile by tim.booth ▴ 60
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
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