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1,000 results • Page 1 of 20
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15
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15
replies
23k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 8 weeks ago by 37k • written 6.7 years ago by ▴ 180
4
votes
13
replies
20k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 12 weeks ago by • 0 • written 4.6 years ago by ▴ 20
2
votes
8
replies
15k
views
Using vcfutils.pl command
alignment
updated 5 months ago by 37k • written 7.6 years ago by ▴ 40
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 5 months ago by 37k • written 7.6 years ago by ▴ 920
27
votes
17
replies
14k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
9 months ago by Leite ★ 1.2k
0
votes
3
replies
13k
views
How to choose a TPM cut-off point
RNA-Seq transcript tpm
updated 5 weeks ago by 37k • written 6.9 years ago by ▴ 10
1
vote
8
replies
13k
views
HTSeq-count high number of no_feature
htseq-count rna-seq
updated 5 months ago by 37k • written 7.6 years ago by ▴ 80
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi nBLAST linux blast
updated 23 days ago by 37k • written 7.0 years ago by ★ 1.2k
3
votes
11
replies
11k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 5 months ago by 37k • written 7.7 years ago by ▴ 120
3
votes
1
reply
10k
views
Negative P-Values
gene genome next-gen-sequencing
updated 6 weeks ago by 37k • written 7.1 years ago by ▴ 200
2
votes
0
replies
9.6k
views
How to plot UniFrac PCoA with 95% confidence Elipses in R
metagenomics ordiellipse vegan R phyloseq
updated 6 months ago by 37k • written 7.7 years ago by ▴ 100
2
votes
4
replies
9.6k
views
Pymol-Generate Pymol Movie To Mpeg
pymol
updated 8 months ago by 37k • written 10.7 years ago by ▴ 530
11
votes
10
replies
9.6k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT RNA-Seq
updated 9 months ago by 37k • written 8.1 years ago by ▴ 160
2
votes
16
replies
9.1k
views
Tophat with Bowtie2 long index
tophat bowtie
updated 8 months ago by 37k • written 8.2 years ago by ▴ 130
3
votes
10
replies
8.8k
views
How can I obtain SNP from TCGA?
Risky-allele BRCA SNP
updated 8 months ago by 37k • written 8.0 years ago by ▴ 10
3
votes
6
replies
8.7k
views
6 follow
How to calculate genetic correlation with R
R
updated 4 months ago by • 0 • written 8.4 years ago by ▴ 80
10
votes
11
replies
8.0k
views
How to adjust my manhattan plot to look better?
qqman manhattan R
updated 4 months ago by 37k • written 7.5 years ago by ▴ 40
1
vote
6
replies
8.0k
views
How to use python to process .CEL file?
cel affymetrix python R cmap
updated 4 months ago by 37k • written 7.6 years ago by ▴ 110
4
votes
6
replies
7.7k
views
Spades assembler output
Assembly
updated 8 weeks ago by 37k • written 6.7 years ago by ▴ 30
2
votes
9
replies
7.7k
views
How to highlight genes on a Manhattan plot
R gene SNP
updated 9 months ago by 37k • written 8.1 years ago by • 0
2
votes
2
replies
7.6k
views
How to filter out special sequences from a fasta file based on sequence IDs txt
fasta
updated 29 days ago by 37k • written 7.0 years ago by ▴ 130
2
votes
12
replies
7.5k
views
8 follow
michigan imputation server
conversion michigan imputation server
updated 10 months ago by • 0 • written 4.6 years ago by ▴ 20
2
votes
7
replies
7.5k
views
linux 'cat' command merge fasta files without headers
cat linux concatenate fasta files bioinformatics
updated 11 months ago by 37k • written 8.3 years ago by • 0
4
votes
3
replies
7.4k
views
Convert Tab delimited file to VCF file
snp
updated 4 months ago by 37k • written 7.0 years ago by • 0
11
votes
29
replies
7.4k
views
SummarizedExperiment nrow differs from ncol
DESeq2 SummarizedExperiment
updated 11 months ago by 37k • written 8.3 years ago by ★ 1.6k
5
votes
4
replies
7.4k
views
GFF3 to GTF conversion - 9th column
gtf NCBI gff3 featureCounts
updated 8 weeks ago by 37k • written 6.7 years ago by ▴ 50
7
votes
18
replies
7.3k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 7 months ago by 37k • written 7.9 years ago by ▴ 190
3
votes
7
replies
7.0k
views
RNA-STAR, mapping problem (number of reads)
RNA-Seq
updated 11 weeks ago by 37k • written 6.6 years ago by • 0
5
votes
15
replies
6.8k
views
Strand specific protocol for bowtie2 alignment
bowtie2 rnaseq alignment RNA-Seq
updated 10 months ago by 37k • written 6.9 years ago by ▴ 90
1
vote
7
replies
6.7k
views
Unaligned Reads From Bowtie2
bowtie2
updated 9 months ago by 37k • written 8.9 years ago by ▴ 360
2
votes
4
replies
6.6k
views
how can I make input file for Haploview from Output files of inferred haplotypes by fastPHASE?
Haploview phased-haplotypes fastPHASE
updated 10 months ago by 37k • written 8.2 years ago by ▴ 210
1
vote
6
replies
6.6k
views
using bcftools/samtools to generate consensus using reference + variants; output is a truncated reference
samtools bcftools mosaik consensus rc454
updated 4 months ago by 37k • written 7.5 years ago by ▴ 10
1
vote
5
replies
6.6k
views
Java Error "Concurrent.Executionexception" While Running Trimmomatic V0.32
java qualitycontrol
updated 9 months ago by 37k • written 8.7 years ago by ★ 1.8k
4
votes
7
replies
6.5k
views
How to create chain file to change genome coordinates from one genome version to another
remap liftover chain-format
updated 6 months ago by 37k • written 8.0 years ago by ★ 4.7k
4
votes
2
replies
6.4k
views
PLINK Merge error: File write failure
plink 1000genomes
updated 4 weeks ago by 37k • written 7.0 years ago by ▴ 70
0
votes
4
replies
6.4k
views
Problem With Autodock 4.2.5
docking
updated 6 months ago by 37k • written 9.8 years ago by ▴ 70
0
votes
0
replies
6.4k
views
Error in grid.Call.graphics(L_setviewport, vp, TRUE) : non-finite location and/or size for viewport
gviz
updated 10 weeks ago by 37k • written 7.0 years ago by • 0
0
votes
2
replies
6.4k
views
High light specific dot in scatterplot
R
updated 7 months ago by 37k • written 7.9 years ago by ▴ 160
6
votes
3
replies
6.4k
views
How to set a threshold for coefficient of variation in RNA-seq?
dispersion statistics single-cell RNA-Seq variance
updated 6 months ago by 37k • written 7.7 years ago by ▴ 250
0
votes
2
replies
6.4k
views
Illumina adapter diagram
illumina sequencing adapter-trimming
updated 3 months ago by 37k • written 7.5 years ago by • 0
2
votes
5
replies
6.3k
views
Tophat Protocol Error Occured At Step 4
tophat rna-seq
updated 4 months ago by 37k • written 10.3 years ago by ▴ 100
3
votes
5
replies
6.3k
views
Visualising the number of overlapping peaks in ChIP-seq studies
ChIP-Seq
updated 10 weeks ago by 37k • written 6.6 years ago by ★ 3.3k
2
votes
6
replies
6.2k
views
PLINK returns NA values for all minor allele frequencies in my data
freq plink maf SNP
updated 8 months ago by 37k • written 8.0 years ago by ▴ 60
2
votes
1
reply
6.2k
views
Difference between UPGMA and the NJ
UPGMA phylogenetics NJ
updated 7 months ago by 37k • written 7.8 years ago by ▴ 10
7
votes
19
replies
6.0k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray R
updated 8 months ago by 37k • written 7.9 years ago by ▴ 10
5
votes
22
replies
6.0k
views
SVM for classified gene expression data
R svm microarray
updated 8 weeks ago by 37k • written 6.7 years ago by ▴ 50
5
votes
11
replies
6.0k
views
Error while running miso
RNA-Seq splicing
updated 8 weeks ago by 37k • written 7.1 years ago by ▴ 40
0
votes
3
replies
6.0k
views
Cross validation error Admixture
SNP software-error
updated 4 months ago by 37k • written 7.6 years ago by • 0
7
votes
9
replies
5.9k
views
Converting Gene Predictions In Glimmer To Protein Sequences.
script biopython
updated 8 months ago by 37k • written 9.2 years ago by ▴ 50
2
votes
3
replies
5.9k
views
bwa mem failed to allocate memory
bwa-mem bwa
updated 6 months ago by 37k • written 7.7 years ago by ▴ 90
1,000 results • Page 1 of 20
Recent Votes
A: Deseq Analysis With Two Samples Without Replicates, Most Padj Equal To 1 And Na
Answer: "RNA-seq by Example" Differential Gene Expression Error
Answer: "RNA-seq by Example" Differential Gene Expression Error
Answer: Microarray DEG analysis visualisation
C: differential expression analysis with DESeq2 & edgeR
Answer: Are alternative splicing analysis and differential expression analysis of RNA-se
differential expression analysis with DESeq2 & edgeR
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Recent Replies
Comment: Can we use UMAP clustering on bulk data? by 5heikki 10k
If you have a distance matrix of some sort, I recommend that you try affinity propagation..
Comment: Is there a tutorial/ demo on single cell nuclei-seq analysis by Emily ▴ 30
Is there a python version or currently only available in R?
Comment: In GWAS Analysis, my top most significant SNPs from pre-imputation data does not by debleena.guin • 0
We did not perform multiple correction. The SNPs significant pre-imputation (unadjusted p < 1x10-16) is no longer significant post imputati…
Answer: Deseq Analysis With Two Samples Without Replicates, Most Padj Equal To 1 And Na by rutuja.digraskar • 0
NOIseq gave me good results with foldchange and expression difference for no replicates.. I used the following tutorial: https://jiankaiwa…
Comment: combine headers from two fata files by emiliomastriani ▴ 30
Thanks iraun. The merger line is perfect.
Comment: My ensembl requests are suddenly very slow - why? by ngarber ▴ 50
No need, that can't be the problem because it doesn't always die at that particular ID - sometimes it dies after only a couple! It never ge…
Comment: Convert Gene Ensemble IDs to Gene Symbols on R by igor 13k
Novel genes used to be assigned temporary cryptic placeholder symbols like AC010680.1 or LINC02050 or C1orf43. They recently stopped doing …
Comment: "RNA-seq by Example" Differential Gene Expression Error by Jeremy ▴ 590
Got it. I missed that update. Thanks a lot!
Comment: My ensembl requests are suddenly very slow - why? by GenoMax 120k
Perhaps there is an error in the compara database for that entry. Can you remove that and see if your job proceeds?
Comment: My ensembl requests are suddenly very slow - why? by ngarber ▴ 50
It shows as error 503: "service unavailable" when I click that link... also, here's a strange thing, I just tried from another internet con…
Answer: Kraken 2 example txt files by Istvan Albert 94k
There is a new paper out on Kraken 2, they ought to have some results: * Metagenome analysis using the Kraken software suite https://…
Comment: My ensembl requests are suddenly very slow - why? by GenoMax 120k
That ID does have homologs available: https://usa.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000185104;r=1:50437028-509…
Answer: "RNA-seq by Example" Differential Gene Expression Error by GenoMax 120k
You create the `design.csv` file using an editor in step 3 of the step-by-step process. It needs to contain the following: sample,co…
Comment: Dramatic decrease of mapping efficiency between Bwameth and Bismark by reza.jabal ▴ 560
What model organism are you using in your experiment? Human, model organism or non-model organism?
Comment: Ensembl Homology REST requests - possible to download whole database and query l by ngarber ▴ 50
So for looking at homologs of human proteins, do I want the following file? http://ftp.ensembl.org/pub/current_compara/conservation_sc…
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