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23
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22
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38k
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 3 months ago by • 0 • written 4.9 years ago by ▴ 250
4
votes
4
replies
33k
views
How to convert a URL into a DOI programmatically
pubmed doi url
written 6.5 years ago by ▴ 100
20
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 7 months ago by 38k • written 7.2 years ago by ▴ 190
4
votes
13
replies
25k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 8 months ago by • 0 • written 5.1 years ago by ▴ 20
4
votes
6
replies
23k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools linux data
3.9 years ago by star ▴ 330
1
vote
3
replies
23k
views
How to extract vcf.gz and vcf.gz.tbi
SNP sequence gene
updated 4.7 years ago by 153k • written 4.7 years ago by ▴ 20
3
votes
4
replies
21k
views
Using nr database for BLAST search
nr database blast blastp
updated 6.6 years ago by 20 • written 6.7 years ago by ▴ 20
9
votes
4
replies
20k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
5.9 years ago by ariel.balter ▴ 190
2
votes
4
replies
20k
views
Error in file(file, "rt") : cannot open the connection
R MicroRNA TXT FORMAT
updated 7.0 years ago by 127k • written 7.0 years ago by • 0
1
vote
5
replies
17k
views
Calculating the sequence similarity and percentage of matched sequences
alignment sequence
updated 5.3 years ago by • 0 • written 5.4 years ago by ▴ 10
7
votes
16
replies
17k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
6.7 years ago by aggregatibacter ▴ 170
27
votes
17
replies
16k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
15 months ago by Leite ★ 1.2k
2
votes
8
replies
16k
views
Using vcfutils.pl command
alignment
updated 11 months ago by 38k • written 8.1 years ago by ▴ 40
2
votes
10
replies
16k
views
How do you use the Aspera ascp command?
aspera gigascience gigaDb
updated 18 months ago by 38k • written 7.5 years ago by ▴ 940
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 11 months ago by 38k • written 8.1 years ago by ▴ 920
2
votes
13
replies
15k
views
convert text file to fasta file
blast
updated 6.6 years ago by 12k • written 6.6 years ago by ▴ 30
6
votes
2
replies
15k
views
Pacbio Ccs Vs Subreads Explained ?
updated 8.9 years ago by 20 • written 9.4 years ago by ▴ 40
0
votes
8
replies
15k
views
find ORF in sequence python
sequence
updated 6.2 years ago by ★ 3.9k • written 6.3 years ago by ▴ 120
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE insert-size
6.7 years ago by Ric ▴ 430
2
votes
3
replies
15k
views
Subsetting - Raw Counts from Seurat Object
seurat raw counts RNA-Seq
2.9 years ago by David_emir ▴ 460
4
votes
10
replies
14k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 4.9 years ago by 127k • written 4.9 years ago by ▴ 720
0
votes
3
replies
14k
views
How to choose a TPM cut-off point
RNA-Seq transcript tpm
updated 7 months ago by 38k • written 7.4 years ago by ▴ 10
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
4.8 years ago by salamandra ▴ 530
5
votes
4
replies
14k
views
glmnet package lasso error
glmnet lasso multilinear regression
5.1 years ago by demoraesdiogo2017 ▴ 90
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
8.8 years ago by ira_grich • 0
2
votes
4
replies
14k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 5 months ago by 38k • written 7.7 years ago by ▴ 10
3
votes
1
reply
13k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq TPM STAR salmon quantification
6.2 years ago by ZheFrench ▴ 500
1
vote
8
replies
13k
views
HTSeq-count high number of no_feature
htseq-count rna-seq
updated 11 months ago by 38k • written 8.1 years ago by ▴ 80
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 4.6 years ago by 38k • written 7.1 years ago by ▴ 50
9
votes
13
replies
13k
views
GC Content of Fasta file --- Python Help
sequence
6.1 years ago by Patrick Brennan ▴ 50
7
votes
4
replies
13k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 3.4 years ago by • 0 • written 5.7 years ago by ▴ 130
0
votes
2
replies
13k
views
Error in -delete: invalid argument to unary operator
RNA-Seq R
3.1 years ago by ovariohisterectomia ▴ 40
1
vote
5
replies
12k
views
pheatmap: how to use legend information as row annotation?
R pheatmap legend annotation
5.0 years ago by n85825 • 0
3
votes
8
replies
12k
views
Error when running pheatmap
pheatmap Error in hclust
4.0 years ago by luzglongoria ▴ 40
6
votes
13
replies
12k
views
Fastq file is truncated error message
RNA-Seq error fastq
6.8 years ago by rob.costa1234 ▴ 310
6
votes
13
replies
12k
views
Showing FDR and log2FC in Volcano plot using R
R RNA-Seq volcano plot
updated 3.8 years ago by 11k • written 5.3 years ago by ★ 3.4k
0
votes
2
replies
12k
views
How to download pfam database
sequence
updated 6.2 years ago by 9.5k • written 6.2 years ago by ▴ 30
0
votes
4
replies
12k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 5 months ago by 38k • written 7.6 years ago by ▴ 10
4
votes
1
reply
12k
views
Converting BigBed to Bed format
Installing BigFile Support
7.8 years ago by sumaira.zaman10 ▴ 20
9
votes
13
replies
12k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
3.6 years ago by Arindam Ghosh ▴ 470
3
votes
11
replies
12k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 11 months ago by 38k • written 8.2 years ago by ▴ 120
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi nBLAST linux blast
updated 6 months ago by 38k • written 7.5 years ago by ★ 1.2k
9
votes
13
replies
12k
views
Sort bam file by coordinates using samtools
sequencing next-gen gene rna-seq Tool
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 30
4
votes
18
replies
12k
views
Alignment with BWA and SAMtools
BWA SAM-file SAMtools
updated 2.4 years ago by 20 • written 4.6 years ago by ▴ 30
1
vote
2
replies
12k
views
kart file in prefetch
rna-seq
updated 6.4 years ago by 20 • written 6.6 years ago by ▴ 20
0
votes
1
reply
11k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 6.7 years ago by 20 • written 6.7 years ago by ▴ 80
0
votes
3
replies
11k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python file-handeling
6.9 years ago by BioICoder ▴ 40
0
votes
2
replies
11k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq GSEA gene genome
updated 3.7 years ago by ▴ 330 • written 3.7 years ago by • 0
4
votes
12
replies
11k
views
STAR alignment error- Segmentation fault (core dumped)
alignment software error RNA-Seq STAR
4.7 years ago by EagleEye 7.4k
3
votes
2
replies
11k
views
ExAC PLI score calculation
DNA-Seq
6.1 years ago by jonessara770 ▴ 240
1,000 results • Page 1 of 20
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A: Extract Base Based On Position From Bam File
PyComplexHeatmap: a Python package to visualize multimodal genomics data
pulling snps from vcf file using ids
A: pulling snps from vcf file using ids
Answer: Scaling RNA-Seq data before clustering?
Answer: How to use CAFE from Orthofinder Results
Answer: merge vcf.gz file
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Comment: GO enrichment analysis by Antonio R. Franco ★ 5.0k
I had the same situation that I solved using the R package TopGO. You have already the list of GO terms. Need to follow the instructions i…
Comment: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran by andres.firrincieli 3.1k
Hi @6f8262bb I still have no idea what could be the cause but switching to guppy v6.2 solved this problem
Answer: Dealing with very large gene-lists in GSEA by Trivas ▴ 710
IMO, in those cases you could look at ES instead of NES. Regardless, within the function `fgsea`, you can set the parameters `minSize` and …
Comment: merge vcf.gz file by Mali • 0
file1 = '/sci/labs/orzuk/orzuk/projects/Skin/data/Ichilov/vcfFiles/vcfFiles/eb3_1001_748-gatk-haplotype.final.vcf.gz' file2 = '/sci/labs/or…
Comment: Which GPU for local Colabfold by matt_arnold_bio • 0
Another giveaway is that when you hit run, it will say either "Running on GPU" or "Running on CPU" in the log output... ![enter image desc…
Answer: Which GPU for local Colabfold by matt_arnold_bio • 0
Hi Arjen, This is a little while ago now so maybe this is not that helpful but... You should be able to tell if the GPU is being seen…
Comment: STAR solo set parameters for scrna-seq by t.ru ▴ 20
it's single cell mars-seq. Yes sorry its a fastq file.
Answer: boxplot issue by yura.grabovska ▴ 50
First of all, you're not outputting the result of your scale to anything... t(apply(mat, 1, scale)) colnames(mat) <- rownames(cold…
Comment: STAR solo set parameters for scrna-seq by GenoMax 127k
> a fasta file similar to this This is not a fasta file It is a fastq format file. Are you sure this is single cell RNAseq data? Looking…
Answer: heatmap issue by yura.grabovska ▴ 50
Your controls clearly show variable expression for the genes you're plotting so to get them to stick together on the left, you would need t…
Comment: How to demultiplex single end - dual index run - NextSeq 500 by GenoMax 127k
Correct. This is a single-end dual indexed (8 bp each) run.
Comment: genome annotation [sstart] [send] - how to get protein sequence from gene by danfarkas • 0
Hi shenwei356, Thanks for the clarification. However, I did try this, and it was not yielding the expected amino acid sequences. This is w…
Comment: Artificial reads - remove multiple mapped reads against reference genome, and on by Agamemnon ▴ 60
I ran ```samtools view -F 4 -q 42 test.bam | wc -l``` and I get ```6159141```, why is there a discrepancy, as originally only ```5200484```…
Comment: differential gene analysis by kalyani • 0
okay thankks!
Comment: Kallisto bustools for scRNA-seq by t.ru ▴ 20
@SRR17050039.1 NB501465:544:HF2H7BGXB:1:22104:14442:1233_TCCTGAGC_barcode=NA-EEEE-AAAAAEE-EEEEEEEE-GCTG-TGCCAGA-ACGTTCAT-W202012/1 GCCCTGTA…
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