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23
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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
31k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 17 months ago by • 0 • written 5.7 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 7.2 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 7.6 years ago by 136k • written 7.6 years ago by • 0
27
votes
17
replies
20k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
24 months ago by Leite ★ 1.3k
7
votes
16
replies
19k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
7.3 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 2.2 years ago by 41k • written 8.1 years ago by ▴ 940
16
votes
38
replies
16k
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
5.4 years ago by salamandra ▴ 550
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 6.9 years ago by ★ 3.9k • written 6.9 years ago by ▴ 120
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
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet lasso multilinear regression
5.7 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
5.6 years ago by n85825 • 0
2
votes
4
replies
15k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 13 months ago by 41k • written 8.3 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
3
votes
8
replies
15k
views
Error when running pheatmap
pheatmap Error in hclust
4.7 years ago by luzglongoria ▴ 50
1
vote
8
replies
15k
views
How to update rlang in R?
rlang R
14 months ago by Amr ▴ 140
8
votes
4
replies
14k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 4.0 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 ▴ 150
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 5.2 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 19 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 4.1 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
3.5 years ago by Thorerges ▴ 10
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
4
votes
12
replies
12k
views
STAR alignment error- Segmentation fault (core dumped)
alignment software error RNA-Seq STAR
5.4 years ago by EagleEye 7.5k
0
votes
2
replies
12k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq GSEA gene genome
updated 4.3 years ago by ▴ 340 • written 4.3 years ago by • 0
1,000 results • Page 1 of 20
Recent Votes
Comment: How Can I move the scattered dots more closer into the center of box ?
Answer: How to compare two Seurat object (sample) in order to find top markers?
Answer: Generating consensus sequence from bam file
Comment: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
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Recent Replies
Comment: How Can I move the scattered dots more closer into the center of box ? by ohtang7 ▴ 40
You're right. I would get help from StackExchange sites and GPT
Answer: Is bisulfite-seq data from different studies comparable with each other? by NextGenSeek • 0
The efficiency of bisulfite treatment itself can differ significantly, so I would definitely not compare bisulfite-seq data from different …
Answer: Issue with genetic QC sex check by kl ▴ 10
After setting set-hh-missing, I have the following boxplot, where a F statistic of 0.91 corresponds to a female in my phenotypic dataset wh…
Comment: Bioinformatics by ATpoint 78k
Converting data from one to another format and repairing gene names turned dates. Yes, great field.
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by GenoMax 136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: …
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated? by swbarnes2 13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by fluke • 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts by Istvan Albert 99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by beausoleilmo ▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by CTLong ▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC by ayasu • 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts by Brian Bushnell 19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
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