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23
votes
22
replies
45k
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 12 months ago by • 0 • written 5.6 years ago by ▴ 250
4
votes
4
replies
38k
views
How to convert a URL into a DOI programmatically
pubmed doi url
written 7.2 years ago by ▴ 100
4
votes
13
replies
32k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 17 months ago by • 0 • written 5.8 years ago by ▴ 20
20
votes
15
replies
28k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 16 months ago by 41k • written 7.9 years ago by ▴ 200
2
votes
3
replies
27k
views
How to extract vcf.gz and vcf.gz.tbi
SNP sequence gene
updated 5.4 years ago by 158k • written 5.4 years ago by ▴ 30
5
votes
6
replies
27k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools linux data
4.6 years ago by star ▴ 350
3
votes
4
replies
22k
views
Using nr database for BLAST search
nr database blast blastp
updated 7.3 years ago by 20 • written 7.4 years ago by ▴ 20
9
votes
4
replies
22k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
6.6 years ago by ariel.balter ▴ 220
2
votes
4
replies
21k
views
Error in file(file, "rt") : cannot open the connection
R MicroRNA TXT FORMAT
updated 7.7 years ago by 136k • written 7.7 years ago by • 0
27
votes
17
replies
20k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
2.0 years ago by Leite ★ 1.3k
7
votes
16
replies
19k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
7.4 years ago by aggregatibacter ▴ 180
3
votes
3
replies
19k
views
Subsetting - Raw Counts from Seurat Object
seurat raw counts RNA-Seq
3.6 years ago by David_emir ▴ 470
1
vote
5
replies
19k
views
Calculating the sequence similarity and percentage of matched sequences
alignment sequence
updated 6.0 years ago by • 0 • written 6.1 years ago by ▴ 10
2
votes
8
replies
17k
views
Using vcfutils.pl command
alignment
updated 19 months ago by 41k • written 8.8 years ago by ▴ 40
2
votes
10
replies
17k
views
How do you use the Aspera ascp command?
aspera gigascience gigaDb
updated 2.3 years ago by 41k • written 8.2 years ago by ▴ 950
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 19 months ago by 41k • written 8.8 years ago by ▴ 920
2
votes
13
replies
16k
views
convert text file to fasta file
blast
updated 7.3 years ago by 12k • written 7.3 years ago by ▴ 30
16
votes
14
replies
16k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
5.5 years ago by salamandra ▴ 550
6
votes
2
replies
16k
views
Pacbio Ccs Vs Subreads Explained ?
updated 9.6 years ago by 20 • written 10.1 years ago by ▴ 40
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 7.0 years ago by ★ 3.9k • written 7.0 years ago by ▴ 120
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet lasso multilinear regression
5.8 years ago by demoraesdiogo2017 ▴ 100
13
votes
13
replies
16k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
4.3 years ago by Arindam Ghosh ▴ 510
0
votes
3
replies
15k
views
How to choose a TPM cut-off point
RNA-Seq transcript tpm
updated 15 months ago by 41k • written 8.1 years ago by ▴ 10
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE insert-size
7.4 years ago by Ric ▴ 430
4
votes
10
replies
15k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 5.6 years ago by 136k • written 5.6 years ago by ▴ 720
1
vote
5
replies
15k
views
pheatmap: how to use legend information as row annotation?
R pheatmap legend annotation
5.7 years ago by n85825 • 0
2
votes
4
replies
15k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 13 months ago by 41k • written 8.4 years ago by ▴ 10
4
votes
18
replies
15k
views
Alignment with BWA and SAMtools
BWA SAM-file SAMtools
updated 3.1 years ago by 20 • written 5.3 years ago by ▴ 30
1
vote
8
replies
15k
views
How to update rlang in R?
rlang R
14 months ago by Amr ▴ 140
3
votes
8
replies
15k
views
Error when running pheatmap
pheatmap Error in hclust
4.7 years ago by luzglongoria ▴ 50
8
votes
4
replies
14k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 4.1 years ago by • 0 • written 6.4 years ago by ▴ 140
1
vote
8
replies
14k
views
HTSeq-count high number of no_feature
htseq-count rna-seq
updated 19 months ago by 41k • written 8.8 years ago by ▴ 80
3
votes
1
reply
14k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq TPM STAR salmon quantification
6.9 years ago by ZheFrench ▴ 540
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
9.5 years ago by ira_grich • 0
9
votes
13
replies
14k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 5 months ago by 41k • written 5.2 years ago by ▴ 30
9
votes
13
replies
14k
views
GC Content of Fasta file --- Python Help
sequence
6.8 years ago by Patrick Brennan ▴ 50
6
votes
13
replies
14k
views
Fastq file is truncated error message
RNA-Seq error fastq
7.5 years ago by rob.costa1234 ▴ 310
4
votes
1
reply
14k
views
Converting BigBed to Bed format
Installing BigFile Support
8.5 years ago by sumaira.zaman10 ▴ 20
0
votes
3
replies
14k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap R RNA-Seq annotations
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 160
0
votes
2
replies
13k
views
Error in -delete: invalid argument to unary operator
RNA-Seq R
3.8 years ago by ovariohisterectomia ▴ 40
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 5.3 years ago by 41k • written 7.8 years ago by ▴ 50
6
votes
13
replies
13k
views
Showing FDR and log2FC in Volcano plot using R
R RNA-Seq volcano plot
updated 4.5 years ago by 11k • written 6.0 years ago by ★ 3.4k
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 6.9 years ago by 9.7k • written 6.9 years ago by ▴ 30
3
votes
11
replies
13k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 20 months ago by 41k • written 8.9 years ago by ▴ 120
1
vote
13
replies
13k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 2.5 years ago by ▴ 560 • written 4.2 years ago by • 0
0
votes
4
replies
13k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 14 months ago by 41k • written 8.3 years ago by ▴ 10
2
votes
1
reply
13k
views
Rename Idents in Seurat Object
RNA-Seq
3.6 years ago by Thorerges ▴ 10
4
votes
12
replies
13k
views
STAR alignment error- Segmentation fault (core dumped)
alignment software error RNA-Seq STAR
5.4 years ago by EagleEye 7.5k
1
vote
2
replies
13k
views
kart file in prefetch
rna-seq
updated 7.1 years ago by 20 • written 7.3 years ago by ▴ 20
0
votes
2
replies
12k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq GSEA gene genome
updated 4.4 years ago by ▴ 340 • written 4.4 years ago by • 0
1,000 results • Page 1 of 20
Recent Votes
Answer: Can't install hisat2 with miniconda
Answer: Can't install hisat2 with miniconda
Answer: iqtree vs raxml
Comment: which statistical test and which package for comapre datasets?
Answer: Bowtie 2 alignment
Answer: GO, KEGG, GSEA analysis with ~5 DEGs
Comment: GATK GetPileupSummaries Java heap space
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Comment: Can't install hisat2 with miniconda by Ozymandeus ▴ 30
Thank you! This fixed the issue.
Comment: Tutorials for Spatial Transcriptomics by CTLong ▴ 50
Although I'm not that into ST, but personally, when I learn a new technology, I usually play around with the data that had already been gen…
Comment: Is interleaved Fastq files the same as interlaced fastq by GenoMax 136k
> SPAdes wants interlaced fastq and BWA-MEM wants interleaved fastq Both programs will accept separate paired-end files. The reads in the …
Comment: which statistical test and which package for comapre datasets? by LauferVA 3.8k
@414fa591 this question is in need of clarification, as @rpolicastro has already said. However, based on what you've written, ***the resea…
Comment: Bowtie 2 alignment by Elizabeth ▴ 30
Thank you so much. I'm getting comparable results now. Appreciate the quick response.
Comment: which statistical test and which package for comapre datasets? by rpolicastro 12k
You should explain your experiment in more detail, such as the hypothesis you are testing and the samples you have to test this.
Comment: which statistical test and which package for comapre datasets? by satva72 • 0
thanks for you comment. I think its possible if we compare the different dataset?! to show that distribution is different between datasets.
Comment: How to display a VCF/BCF file or stream as a paginated table in a python web fra by Jeremy Leipzig 22k
seqr now supports Hail but with a layer of elasticsearch. It does not support TileDB but in theory it could.
Comment: which statistical test and which package for comapre datasets? by Jeremy ▴ 860
I think you will need at least three replicates to be able to do statistics.
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Pierre Lindenbaum 158k
> Asking for bed file is not a suitable option in the current scenario. ???????
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Manuel Sokolov Ravasqueira ▴ 100
they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Pierre Lindenbaum 158k
> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Manuel Sokolov Ravasqueira ▴ 100
thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)
Comment: Is interleaved Fastq files the same as interlaced fastq by rpolicastro 12k
This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…
Comment: Is interleaved Fastq files the same as interlaced fastq by RCMC • 0
Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
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