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23
votes
22
replies
40k
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 6 months ago by • 0 • written 5.1 years ago by ▴ 250
4
votes
4
replies
35k
views
How to convert a URL into a DOI programmatically
pubmed doi url
written 6.7 years ago by ▴ 100
4
votes
13
replies
27k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 11 months ago by • 0 • written 5.3 years ago by ▴ 20
20
votes
15
replies
26k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 10 months ago by 39k • written 7.4 years ago by ▴ 190
4
votes
6
replies
24k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools linux data
4.1 years ago by star ▴ 340
1
vote
3
replies
24k
views
How to extract vcf.gz and vcf.gz.tbi
SNP sequence gene
updated 4.9 years ago by 155k • written 4.9 years ago by ▴ 20
3
votes
4
replies
21k
views
Using nr database for BLAST search
nr database blast blastp
updated 6.8 years ago by 20 • written 6.9 years ago by ▴ 20
9
votes
4
replies
21k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
6.1 years ago by ariel.balter ▴ 200
2
votes
4
replies
20k
views
Error in file(file, "rt") : cannot open the connection
R MicroRNA TXT FORMAT
updated 7.2 years ago by 130k • written 7.2 years ago by • 0
1
vote
5
replies
18k
views
Calculating the sequence similarity and percentage of matched sequences
alignment sequence
updated 5.5 years ago by • 0 • written 5.6 years ago by ▴ 10
7
votes
16
replies
18k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
6.9 years ago by aggregatibacter ▴ 180
27
votes
17
replies
18k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
18 months ago by Leite ★ 1.2k
2
votes
8
replies
17k
views
Using vcfutils.pl command
alignment
updated 13 months ago by 39k • written 8.3 years ago by ▴ 40
2
votes
10
replies
16k
views
How do you use the Aspera ascp command?
aspera gigascience gigaDb
updated 21 months ago by 39k • written 7.7 years ago by ▴ 940
2
votes
3
replies
16k
views
Subsetting - Raw Counts from Seurat Object
seurat raw counts RNA-Seq
3.1 years ago by David_emir ▴ 460
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 13 months ago by 39k • written 8.3 years ago by ▴ 920
2
votes
13
replies
16k
views
convert text file to fasta file
blast
updated 6.8 years ago by 12k • written 6.8 years ago by ▴ 30
6
votes
2
replies
15k
views
Pacbio Ccs Vs Subreads Explained ?
updated 9.1 years ago by 20 • written 9.6 years ago by ▴ 40
0
votes
8
replies
15k
views
find ORF in sequence python
sequence
updated 6.4 years ago by ★ 3.9k • written 6.4 years ago by ▴ 120
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE insert-size
6.9 years ago by Ric ▴ 430
5
votes
4
replies
14k
views
glmnet package lasso error
glmnet lasso multilinear regression
5.3 years ago by demoraesdiogo2017 ▴ 90
4
votes
10
replies
14k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 5.1 years ago by 130k • written 5.1 years ago by ▴ 720
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
5.0 years ago by salamandra ▴ 540
0
votes
3
replies
14k
views
How to choose a TPM cut-off point
RNA-Seq transcript tpm
updated 9 months ago by 39k • written 7.6 years ago by ▴ 10
2
votes
4
replies
14k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 7 months ago by 39k • written 7.9 years ago by ▴ 10
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
9.0 years ago by ira_grich • 0
3
votes
1
reply
14k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq TPM STAR salmon quantification
6.4 years ago by ZheFrench ▴ 520
1
vote
8
replies
14k
views
HTSeq-count high number of no_feature
htseq-count rna-seq
updated 13 months ago by 39k • written 8.3 years ago by ▴ 80
7
votes
4
replies
13k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 3.6 years ago by • 0 • written 5.9 years ago by ▴ 130
1
vote
5
replies
13k
views
pheatmap: how to use legend information as row annotation?
R pheatmap legend annotation
5.2 years ago by n85825 • 0
9
votes
13
replies
13k
views
GC Content of Fasta file --- Python Help
sequence
6.3 years ago by Patrick Brennan ▴ 50
13
votes
13
replies
13k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
3.8 years ago by Arindam Ghosh ▴ 500
3
votes
8
replies
13k
views
Error when running pheatmap
pheatmap Error in hclust
4.2 years ago by luzglongoria ▴ 40
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 4.8 years ago by 39k • written 7.3 years ago by ▴ 50
0
votes
2
replies
13k
views
Error in -delete: invalid argument to unary operator
RNA-Seq R
3.3 years ago by ovariohisterectomia ▴ 40
6
votes
13
replies
13k
views
Fastq file is truncated error message
RNA-Seq error fastq
7.0 years ago by rob.costa1234 ▴ 310
4
votes
1
reply
13k
views
Converting BigBed to Bed format
Installing BigFile Support
8.0 years ago by sumaira.zaman10 ▴ 20
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 6.4 years ago by 9.6k • written 6.4 years ago by ▴ 30
4
votes
18
replies
13k
views
Alignment with BWA and SAMtools
BWA SAM-file SAMtools
updated 2.6 years ago by 20 • written 4.8 years ago by ▴ 30
6
votes
13
replies
12k
views
Showing FDR and log2FC in Volcano plot using R
R RNA-Seq volcano plot
updated 4.0 years ago by 11k • written 5.5 years ago by ★ 3.4k
9
votes
13
replies
12k
views
Sort bam file by coordinates using samtools
sequencing next-gen gene rna-seq Tool
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 30
0
votes
4
replies
12k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 8 months ago by 39k • written 7.8 years ago by ▴ 10
3
votes
11
replies
12k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 14 months ago by 39k • written 8.4 years ago by ▴ 120
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi nBLAST linux blast
updated 9 months ago by 39k • written 7.7 years ago by ★ 1.2k
1
vote
2
replies
12k
views
kart file in prefetch
rna-seq
updated 6.6 years ago by 20 • written 6.8 years ago by ▴ 20
0
votes
3
replies
12k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap R RNA-Seq annotations
updated 3.0 years ago by 39k • written 3.0 years ago by ▴ 130
0
votes
2
replies
12k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq GSEA gene genome
updated 3.9 years ago by ▴ 340 • written 3.9 years ago by • 0
0
votes
1
reply
12k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 6.9 years ago by 20 • written 6.9 years ago by ▴ 90
4
votes
12
replies
12k
views
STAR alignment error- Segmentation fault (core dumped)
alignment software error RNA-Seq STAR
4.9 years ago by EagleEye 7.5k
2
votes
1
reply
11k
views
Rename Idents in Seurat Object
RNA-Seq
3.1 years ago by Thorerges ▴ 10
1,000 results • Page 1 of 20
Recent Votes
Differences between trimming tools: cutadapt, bbduk and sickle
C: How sickle (adaptive trimming tool) work.
How sickle (adaptive trimming tool) work.
Comment: Help with running ATAC using Encode pipeline
Answer: Is there a file format better suited for the era of pangenomics than the .vcf? W
Answer: Is there a file format better suited for the era of pangenomics than the .vcf? W
A: Can EdgeR of DeSeq be used for Single-cell RNA-seq?
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Popular Question to kenneditodd ▴ 10
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Recent Replies
Answer: multiqc: group samples by population + boxplot ? by Phil Ewels ★ 1.2k
You can't group and make boxplots as you describe, probably your best bet is to use the [highlight tool][1] in the report (especially if yo…
Comment: Problem with GPU guppy_basecaller and SLURM by kenneditodd ▴ 10
Nope - but I just noticed another error message in the guppy log. I've seen some people have the same problem on nanopore community but not…
Comment: Where to get the molecular subtype information of STAD sample in TCGA by younglin113 ▴ 50
Thanks a lot! But still a bit curious why this information is not included in GDC or UCSC xena.
Comment: CellRanger problem by Carlos Eduardo • 0
I'm using cellranger mkref --genome=Viral --fasta=path.fna --genes=path.gtf I have 126G RAM
Comment: How do I run DE for TPM values (not CPM)? by John • 0
Thanks, but it's giving me the error that expression object should be numeric and that there are 2 non-numeric columns (because the first t…
Comment: How do I run DE for TPM values (not CPM)? by LChart 2.7k
you're mixing two packages, edgeR ("dgelist") and limma ("lmFit"). Just put your log(1+TPM) matrix as the first argument to lmFit.
Answer: hisat2-align exited with value 1 by GenoMax 130k
You only need to use the `basename` of the index when you specify it. Try hisat2 -p 4 -x /home/ngs/zebra_fish/zebra_fish -U SRR10480…
Comment: How to deal with SRA file without .SRA by Andy ▴ 50
Thank you Ram! Yes, I did something wrong.
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W by Ram 39k
Exactly. Even when we were trying to leverage hail at my previous job, we ran into troubles constantly with data freezes. IMO academia is n…
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W by Jeremy Leipzig 21k
OK hospitals in particular definitely don't want to regenerate anything as individual new samples are added to the variant store. Even the …
Comment: How to deal with SRA file without .SRA by Ram 39k
PRJNA is the standard NCBI BioProject prefix. There are 19 pairs of FASTQs associated with this one so you're doing something wrong
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W by Ram 39k
> But you can't live out of your suitcase forever. I'd compare it to a local department store vs Walmart - I think cloud/distributed stora…
Comment: How do I run DE for TPM values (not CPM)? by John • 0
That's what I'm trying to do but again, I'm getting an error on the last line and I'm asking how to fix it.
Answer: no output from GATK CombineGVCFs by Vitis ★ 2.5k
The number of gVCFs in the list has a hard limit (interestingly I don't exactly know this number as it changes with different GATK versions…
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W by Matthias Zepper 3.7k
I see, how the importance of genomic coordinates and fixed-length scaffolds decreases if pangenomic references are to become the norm, yet …
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