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200 results • Page 1 of 4
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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
13
votes
14
replies
805
views
High Malat-1 expression in single cell data
single-cell
updated 2 days ago by ▴ 40 • written 10 days ago by ▴ 40
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
293
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 1 day ago by ▴ 180 • written 2 days ago by • 0
10
votes
14
replies
657
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 2 days ago by 142k • written 8 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
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 4 days ago by ▴ 10 • written 24 months ago by • 0
5
votes
2
replies
75
views
EdgeR - relationship between logFC and coefficients
differential-expression r edger
updated 1 hour ago by ★ 7.1k • written 4 hours ago by ▴ 10
5
votes
5
replies
265
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
2 days ago by Chris ▴ 280
5
votes
5
replies
622
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 6 days ago by • 0 • written 15 days ago by ★ 3.9k
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 17 hours ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 3 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
2
replies
260
views
GRCh38.gmap file
gnomix gmap
5 days ago by lorena9132 ▴ 10
4
votes
2
replies
245
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 5 days ago by 43k • written 6 days ago by ▴ 40
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 6 days ago by ★ 7.1k • written 4 months ago by ▴ 10
4
votes
1
reply
237
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 3 days ago by 11k • written 5 days ago by ▴ 560
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 1 day ago by ▴ 90 • written 6.4 years ago by ▴ 60
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 6 days ago by • 0 • written 2.2 years ago by • 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 1 day ago by ▴ 10 • written 2.5 years ago by • 0
4
votes
2
replies
243
views
How can I analyze normalized expression data?
DEseq2 RNA-seq
1 day ago by mnx0723 • 0
4
votes
3
replies
1.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 19 hours ago by 161k • written 21 hours ago by ★ 1.2k
3
votes
8
replies
525
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
3 days ago by Qroid ▴ 40
3
votes
3
replies
337
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 6 days ago by 82k • written 7 days ago by • 0
3
votes
4
replies
421
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 3 days ago by ★ 7.1k • written 6 days ago by ▴ 40
3
votes
5
replies
290
views
Generating mpileup file using samtools
mpileup samtools
updated 6 days ago by 21k • written 6 days ago by • 0
3
votes
8
replies
604
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 3 days ago by ▴ 410 • written 7 days ago by ▴ 100
3
votes
3
replies
410
views
absolute path for symbolic links in Snakefile
Snakemake
updated 9 hours ago by ▴ 770 • written 20 days ago by ▴ 60
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 1 day ago by • 0 • written 5.5 years ago by 8.4k
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
4 days ago by Ibrahim Tanyalcin ★ 1.2k
3
votes
5
replies
341
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
6 days ago by Maverick ▴ 10
3
votes
3
replies
232
views
Gene Specific coverage from WGS data
linux WGS Bioinformatics SARS CoV2
3 days ago by Adyasha • 0
2
votes
5
replies
233
views
Importing a fastq file
Fastq
updated 4 hours ago by ▴ 120 • written 1 day ago by • 0
2
votes
1
reply
305
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 6 days ago by 10k • written 9 days ago by ▴ 10
2
votes
4
replies
281
views
RNA seq analysis
DESeq RNA-seq
updated 12 hours ago by • 0 • written 1 day ago by ▴ 10
2
votes
0
replies
53
views
News: course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics SNPs LocalAdaptation GIS
12 hours ago by carlopecoraro2 ★ 2.5k
2
votes
2
replies
323
views
Association study using SNP data
Association Allele Parentage SNP
4 days ago by drajangirija • 0
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 1 day ago by • 0 • written 5.1 years ago by ★ 1.8k
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR statistical test parametric non-parametric
updated 6 days ago by ▴ 210 • written 3.8 years ago by ▴ 40
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
2
replies
221
views
Raw counts using stringtie
stringtie RNA-seq
updated 6 days ago by 142k • written 6 days ago by • 0
2
votes
2
replies
162
views
Is therer any suggestions on mapping rate of WGBS data?
mapping read alignment WGBS
2 days ago by Zeng Jingyu ▴ 60
2
votes
3
replies
821
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 5 days ago by • 0 • written 7 months ago by • 0
2
votes
3
replies
295
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 6 days ago by ★ 1.9k • written 7 days ago by ▴ 30
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 5 days ago by • 0 • written 10.2 years ago by ▴ 20
2
votes
2
replies
237
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB protein STRING-DB-API
4 days ago by brandon • 0
2
votes
4
replies
712
views
Count all variants from vcf file
variants vcf Count
updated 2 days ago by 161k • written 20 months ago by • 0
2
votes
1
reply
125
views
java out of memory error through beagle for imutation
beagle java.out.of.memory imputation
2 days ago by analyst ▴ 50
1
vote
2
replies
222
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 3 days ago by 11k • written 3 days ago by • 0
1
vote
2
replies
304
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
3 days ago by M. ▴ 30
1
vote
2
replies
163
views
Where to get the following bed file?
WES bed reference file
updated 3 days ago by 142k • written 3 days ago by • 0
200 results • Page 1 of 4
Recent Votes
Comment: Importing a fastq file
EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
Detecting highly variable genes within replicates
Detecting highly variable genes within replicates
A: Detecting highly variable genes within replicates
How to set a threshold for coefficient of variation in RNA-seq?
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Recent Replies
Comment: LncRNA Nomenclature by jain72744 ▴ 10
My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
Answer: DESeq2 error by ATpoint 82k
At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
Comment: When should I use R-MarkDown over R-Script ? by ATpoint 82k
What is your motivation to ask? Add some context. Beyond that, always use Rmd unless you write package code.
Comment: LncRNA Nomenclature by ATpoint 82k
RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients by gBioStar5 ▴ 10
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients by Gordon Smyth ★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
Answer: Importing a fastq file by size_t ▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
Comment: Contig assembly task, errors by Philipp Bayer 8.4k
Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
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?
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