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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
31k
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 7.6 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
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
5.4 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 6.9 years ago by ★ 3.9k • written 6.9 years ago by ▴ 120
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
5.7 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
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 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
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
13k
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
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Comment: 4 Fastq files for a single run generated by 10X
Comment: 4 Fastq files for a single run generated by 10X
Answer: How do you generate TMM normalized counts using EdgeR?
The Biostar Handbook. A bioinformatics e-book for beginners.
GEO dataset Microarray data analysis help
C: Batch effects : ComBat or removebatcheffects (limma package) ?
Answer: Batch effects : ComBat or removebatcheffects (limma package) ?
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Comment: 4 Fastq files for a single run generated by 10X by hkarakurt ▴ 180
Thank you for your detailed answer. I will check the reads and compare them with chemistry manual as you suggested. Thank you again for yo…
Comment: Microarray batch correction method suggestions by Sumeet • 0
Thank you @atpoint for your response. However, aim of analysing to generate a matrix with all dataset available after batch correction.
Comment: what should I do if I get a compromised sample of scRNA-seq data? by ATpoint 78k
Agreed. I would just force the cells to 5000 or so, and then proceed with the normal QC. If there's a lot of trash "cells" in the dataset t…
Comment: How to download multiple genome files using command line (MacOS) using datasets by rj.rezwan • 0
you should use the `wild cards` to download all the given above GCF files. Moverover, you can use the commands of `curl` , `wget` and `slow…
Comment: Microarray batch correction method suggestions by ATpoint 78k
This has been asked so many times before. Analyse them separately, then make a statement on reproducibility of results using a meta-analysi…
Comment: Microbial gene coverage from blast result by aanchal.yadav • 0
What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi by Jeremy ▴ 860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread by peanut • 0
Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program…
Comment: Help with gatk CreateSequenceDictionary by Chris ▴ 230
It worked! Thanks Matt!
Comment: Finding human .vcf files online to download by cmdcolin ★ 3.4k
i can't really tell you why your code doesn't work if you dont provide it. and, if you describe as much as possible what your goals are, th…
Answer: Help with gatk CreateSequenceDictionary by MatthewP ★ 1.3k
maybe try?: -R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg3…
Comment: Java error while running HiCDC overview code by Brian Bushnell 20k
Looks like you have corrupt or improperly-formatted input. It's expecting to parse a floating-point number where the word "score" appears.…
Comment: what should I do if I get a compromised sample of scRNA-seq data? by dsull ★ 5.1k
The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a Q…
Comment: Annotation GTF/GFF Arabidopsis thaliana by enriquesan • 0
...........
Comment: FastQC without yellow box by lobelino • 0
Thank you for your answer.
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