Limit : all time
all time today this week this month this year
1,000 results • Page 1 of 20
Sort: Views
Rank Views Votes Replies
23
votes
22
replies
49k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink vcf fam gatk vcftools
updated 16 months ago by • 0 • written 5.9 years ago by ▴ 260
4
votes
4
replies
41k
views
How to convert a URL into a DOI programmatically
pubmed doi url
written 7.6 years ago by ▴ 100
4
votes
13
replies
34k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 21 months ago by ▴ 10 • written 6.1 years ago by ▴ 20
20
votes
15
replies
29k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 20 months ago by 43k • written 8.3 years ago by ▴ 200
5
votes
6
replies
28k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools linux data
5.0 years ago by star ▴ 350
2
votes
3
replies
28k
views
How to extract vcf.gz and vcf.gz.tbi
SNP sequence gene
updated 5.8 years ago by 161k • written 5.8 years ago by ▴ 30
3
votes
4
replies
23k
views
Using nr database for BLAST search
nr database blast blastp
updated 7.6 years ago by 20 • written 7.7 years ago by ▴ 20
11
votes
4
replies
23k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
7.0 years ago by ariel.balter ▴ 250
28
votes
17
replies
21k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
2.4 years ago by Leite ★ 1.3k
3
votes
3
replies
21k
views
Subsetting - Raw Counts from Seurat Object
seurat raw counts RNA-Seq
4.0 years ago by David_emir ▴ 490
2
votes
4
replies
21k
views
Error in file(file, "rt") : cannot open the connection
R MicroRNA TXT FORMAT
updated 8.0 years ago by 141k • written 8.0 years ago by • 0
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
7.7 years ago by aggregatibacter ▴ 180
1
vote
5
replies
19k
views
Calculating the sequence similarity and percentage of matched sequences
alignment sequence
updated 6.4 years ago by • 0 • written 6.4 years ago by ▴ 10
2
votes
8
replies
18k
views
Using vcfutils.pl command
alignment
updated 24 months ago by 43k • written 9.2 years ago by ▴ 40
2
votes
10
replies
18k
views
How do you use the Aspera ascp command?
aspera gigascience gigaDb
updated 2.6 years ago by 43k • written 8.5 years ago by ▴ 950
13
votes
13
replies
17k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
4.7 years ago by Arindam Ghosh ▴ 510
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 24 months ago by 43k • written 9.2 years ago by ▴ 920
16
votes
14
replies
17k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
5.8 years ago by salamandra ▴ 550
2
votes
13
replies
17k
views
convert text file to fasta file
blast
updated 7.6 years ago by 12k • written 7.6 years ago by ▴ 30
4
votes
18
replies
17k
views
Alignment with BWA and SAMtools
BWA SAM-file SAMtools
updated 3.5 years ago by 20 • written 5.7 years ago by ▴ 30
1
vote
8
replies
17k
views
How to update rlang in R?
rlang R
18 months ago by Amr ▴ 160
1
vote
5
replies
16k
views
pheatmap: how to use legend information as row annotation?
R pheatmap legend annotation
6.0 years ago by n85825 • 0
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet lasso multilinear regression
6.1 years ago by demoraesdiogo2017 ▴ 100
0
votes
3
replies
16k
views
How to choose a TPM cut-off point
RNA-Seq transcript tpm
updated 20 months ago by 43k • written 8.5 years ago by ▴ 10
6
votes
2
replies
16k
views
Pacbio Ccs Vs Subreads Explained ?
updated 10.0 years ago by 20 • written 10.5 years ago by ▴ 40
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 7.3 years ago by ★ 4.0k • written 7.3 years ago by ▴ 120
3
votes
8
replies
16k
views
Error when running pheatmap
pheatmap Error in hclust
5.0 years ago by luzglongoria ▴ 50
2
votes
4
replies
16k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 18 months ago by 43k • written 8.7 years ago by ▴ 10
4
votes
10
replies
15k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 6.0 years ago by 141k • written 6.0 years ago by ▴ 750
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE insert-size
7.8 years ago by Ric ▴ 430
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 4.4 years ago by • 0 • written 6.8 years ago by ▴ 140
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 9 months ago by 43k • written 5.6 years ago by ▴ 30
0
votes
3
replies
15k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap R RNA-Seq annotations
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 160
1
vote
8
replies
15k
views
HTSeq-count high number of no_feature
htseq-count rna-seq
updated 24 months ago by 43k • written 9.2 years ago by ▴ 80
4
votes
1
reply
15k
views
Converting BigBed to Bed format
Installing BigFile Support
8.8 years ago by sumaira.zaman10 ▴ 20
4
votes
1
reply
15k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq TPM STAR salmon quantification
7.2 years ago by ZheFrench ▴ 550
6
votes
13
replies
15k
views
Fastq file is truncated error message
RNA-Seq error fastq
7.9 years ago by rob.costa1234 ▴ 310
9
votes
13
replies
15k
views
GC Content of Fasta file --- Python Help
sequence
7.1 years ago by Patrick Brennan ▴ 50
1
vote
13
replies
14k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 2.9 years ago by ▴ 570 • written 4.5 years ago by • 0
0
votes
3
replies
14k
views
Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character
inSilicoMerging
9.9 years ago by ira_grich • 0
0
votes
2
replies
14k
views
Error in -delete: invalid argument to unary operator
RNA-Seq R
4.1 years ago by ovariohisterectomia ▴ 40
6
votes
13
replies
14k
views
Showing FDR and log2FC in Volcano plot using R
R RNA-Seq volcano plot
updated 4.9 years ago by 11k • written 6.4 years ago by ★ 3.4k
8
votes
5
replies
14k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 50
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 7.2 years ago by 9.7k • written 7.2 years ago by ▴ 30
4
votes
12
replies
13k
views
STAR alignment error- Segmentation fault (core dumped)
alignment software error RNA-Seq STAR
5.8 years ago by EagleEye 7.5k
2
votes
1
reply
13k
views
Rename Idents in Seurat Object
RNA-Seq
3.9 years ago by Thorerges ▴ 10
3
votes
11
replies
13k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 130
0
votes
2
replies
13k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq GSEA gene genome
updated 4.7 years ago by ▴ 350 • written 4.7 years ago by • 0
0
votes
4
replies
13k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 18 months ago by 43k • written 8.7 years ago by ▴ 10
1
vote
2
replies
13k
views
kart file in prefetch
rna-seq
updated 7.4 years ago by 20 • written 7.6 years ago by ▴ 20
1,000 results • Page 1 of 20
Recent Votes
Answer: Problem with Sniffles pipeline and SV calling help
A: Need the first and the third element after doing strsplit
OrthoFinder: Diamond or Blast? Which is better?
OrthoFinder: Diamond or Blast? Which is better?
Answer: OrthoFinder: Diamond or Blast? Which is better?
Answer: OrthoFinder: Diamond or Blast? Which is better?
A: Running Blastall Before MCL for Paralog Clustering
Recent Locations • All
WCIP | Glasgow | UK, 1 minute ago
United States, 3 minutes ago
Ambler, 4 minutes ago
United States, 9 minutes ago
India, 9 minutes ago
India, 10 minutes ago
United States, 11 minutes ago
Recent Awards • All
Teacher to Mensur Dlakic ★ 27k
Popular Question to wiscoyogi ▴ 40
Popular Question to tien ▴ 10
Commentator to Alex Reynolds 35k
Popular Question to haiying.kong ▴ 360
Popular Question to Buffo ★ 2.4k
Popular Question to jon.brate ▴ 290
Recent Replies
Comment: Getting marker genes for cell types by orzrzlyo ▴ 20
Thank you! Also, cell typist would successfully identify the above cell types, however, they seemed to be in a pretrained or pre-organized …
Answer: Getting marker genes for cell types by LChart 3.9k
It seems strange that celltypist would not identify these major cell classes -- you should double check your data quality. For the marker l…
Answer: gene body coverage with RSeqQC by jkim ▴ 170
http://qualimap.conesalab.org/doc_html/index.html Never tried rseqc, but qualimap provides a gene body coverage plot also.
Comment: How to get the reference panel sites for TOPMed hg37 and 38 by bk11 ★ 2.3k
You can simply impute your genotyped data in TOPMed server. In that way you do not have to deal with downloading the reference panels (not …
Answer: Using adonis to include a random effect by LChart 3.9k
> why the first model doesn't have stats for both variables? Your variables are multicollinear. This will always be true if you have mul…
Comment: How to row normalize a matrixplot? by bioinfo ▴ 150
Thank you. That is what I ended up doing.
Comment: bash script by Ram 43k
What "error code at the top" are you talking about? Error code in response to the `srun -N 1 -t 0:01:00 bash -c "uname -a"` command? Also, …
Answer: how to get the variance explained by the independent variable from multivariate by LChart 3.9k
More explicitly: ```R G <- mdmr::gower(distance.matrix) eig <- eigen(G) U <- eig$vectors ## this is the MDS embedding matrix lambd…
Comment: bash script by bestone ▴ 30
You write this "I noticed there may be a few parameters required for a SLURM job that could be missing from your script (partition to use, …
Comment: RNAseq 1 control 2 different treatment by sansan_96 ▴ 70
I think what you should do is do differential expression for your two contrasts: treatment 1 vs control and treatment 2 vs control. DESeq2 …
Comment: how to get the variance explained by the independent variable from multivariate by leranwangcs ▴ 120
Thanks for your response! I have no statistics background so a bit hard to figure our the equation you provide with. I just want to find so…
Comment: Extracting information from gff3 file produced by augustus by Istvan Albert 100k
you should be more specific as to what you are trying to do. in general parsing a GFF file, while error prone and annoying it is reasonabl…
Comment: Best way to deal with overlapping read names in merged BAM files by GenoMax 141k
See: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups `\t` is tab <!-- this is a test -->
Comment: Best way to deal with overlapping read names in merged BAM files by shpak.max ▴ 50
Thanks. If I understand correctly, this adds ID1 to the rg header in the first bam, etc. Could you please explain the syntax of the tsM:SAM…
Comment: Best way to deal with overlapping read names in merged BAM files by Pierre Lindenbaum 161k
not tested: samtools addreplacerg -r "@RG\tID:ID1\tSM:SAMPLE1 -O BAM -o new1.bam old1.bam samtools addreplacerg -r "@RG\tID:ID2\tSM:SAM…
Traffic: 1702 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6