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351 results • Page
1 of 8
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1
vote
13
replies
962
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 2 days ago by
lcj34
▴ 410 • written 8 days ago by
b.contreras.moreira
▴ 70
0
votes
12
replies
567
views
BWA MEM different synthax on linux (bash) and macOS (zsh)
MEM
BWA
20 days ago by
gernophil
▴ 80
4
votes
12
replies
3.4k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 1 day ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
0
votes
11
replies
672
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 11 days ago by
barslmn
★ 2.1k • written 22 days ago by
avelarbio46
▴ 30
0
votes
10
replies
771
views
Problem running scPred
scPred
scPredict
updated 14 days ago by
Ram
43k • written 12 weeks ago by
Nitin
• 0
1
vote
10
replies
681
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 7 hours ago by
GenoMax
140k • written 5 weeks ago by
Sky
▴ 10
1
vote
9
replies
1.4k
views
blast retrieves "N/A" for taxonomic data
blast
blastn
updated 18 days ago by
flavianegrete
• 0 • written 3.3 years ago by
langziv
▴ 50
1
vote
9
replies
799
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 15 days ago by
Dave Carlson
★ 1.7k • written 16 days ago by
Matthew
• 0
1
vote
9
replies
440
views
miRNA alignment with Bowtie2
bowtie2
12 days ago by
Chironex
▴ 40
0
votes
8
replies
540
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 29 days ago by
ido.idobar
▴ 10 • written 9 weeks ago by
Elizabeth
▴ 30
2
votes
8
replies
224
views
Piping samtools to R
R
NGS
bash
samtools
15 hours ago by
joe
▴ 470
0
votes
8
replies
351
views
STAR aligner options
STAR
53 minutes ago by
theophile
• 0
0
votes
8
replies
1.4k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 13 days ago by
xiangbinruan
• 0 • written 18 months ago by
Phoebe Magdy
• 0
0
votes
8
replies
404
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
55 minutes ago by
dzisis1986
▴ 70
3
votes
8
replies
560
views
Huge decrease of BUS records using bustools
single-cell
bustools
10X
29 days ago by
julien.wollbrett
• 0
1
vote
7
replies
827
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 1 day ago by
Ram
43k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
2
votes
7
replies
525
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 14 days ago by
Chris Dean
▴ 390 • written 15 days ago by
ev97
▴ 20
3
votes
7
replies
426
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
21 days ago by
Fadlilah
▴ 10
1
vote
7
replies
345
views
Nanopore data filtering using fastp
fastp
nanopore
updated 35 minutes ago by
dthorbur
★ 1.7k • written 2 days ago by
emilydolivo97
• 0
0
votes
7
replies
299
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 11 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
1
vote
7
replies
434
views
limma eBayes error in analysis of Illumina HumanHT-12 V4.0 expression beadchip data
R
beadchip
limma
microarray
Illumina
updated 28 days ago by
1769mkc
★ 1.2k • written 28 days ago by
accibio
▴ 20
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 3 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
0
votes
7
replies
439
views
Using VEP annotation output as the input for a second VEP annotation
VCF
VEP
Annotation
updated 15 days ago by
Ram
43k • written 8 weeks ago by
Arton
• 0
0
votes
7
replies
323
views
single nuclei sequencing questions
fastq
single-nuclei-sequencing
updated 19 days ago by
Ram
43k • written 20 days ago by
Long
• 0
0
votes
7
replies
389
views
Error "ckalloc: request for negative space" about multiz
multiz
23 days ago by
marh32
• 0
2
votes
7
replies
504
views
Need a link to OLDERADO server
pdb
protein
nmr
structure
15 days ago by
b2003
• 0
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
0
votes
6
replies
366
views
Contamination in my FASTQC files
Fastqc
bowtie2
19 days ago by
carlosgonzalezcruz327
▴ 20
2
votes
6
replies
459
views
single cell RNA seq integration(Error in UseMethod(generic = "as.sparse", object = x))
scRNA-seq
19 days ago by
kayah
• 0
4
votes
6
replies
291
views
Protein loops
protein
Loop
13 days ago by
Curious
▴ 10
1
vote
6
replies
1.2k
views
Plots coloring in BPGA pan genome analysis pipeline
genome
next-gen
pan-genome
27 days ago by
hafiz.talhamalik
▴ 350
0
votes
6
replies
486
views
Rooting phylogenetic trees in R using Treeio's root function: Trees don't seem to root.
R
MrBayes
21 days ago by
lingxue
• 0
0
votes
6
replies
369
views
why the file is low after combining the Hi-C reads using Arima genomics pipeline of mapping
bwa
mapping
genome
samtools
plants
19 days ago by
rj.rezwan
• 0
2
votes
6
replies
452
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
5 days ago by
tujuchuanli
▴ 100
0
votes
5
replies
362
views
Issues with bcftools
Bcftools
updated 20 days ago by
Pierre Lindenbaum
160k • written 21 days ago by
hgrsce
• 0
1
vote
5
replies
266
views
Merging bam files from different runs
samtools
bam
updated 16 days ago by
GenoMax
140k • written 16 days ago by
shpak.max
▴ 40
1
vote
5
replies
344
views
How to normalise RNA seq data from two independent experiments to the same scale.
RNAseq
updated 21 days ago by
jv
★ 1.7k • written 22 days ago by
Mo
▴ 40
0
votes
5
replies
350
views
loop string set
python
stringset
updated 22 days ago by
rpolicastro
13k • written 23 days ago by
aj123
▴ 120
0
votes
5
replies
389
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
15 days ago by
Maxwell
▴ 20
0
votes
5
replies
290
views
Bedtools getfasta: error
getfasta
bedtools
updated 16 days ago by
GenoMax
140k • written 16 days ago by
ummeswaiba
• 0
1
vote
5
replies
408
views
Haddock 2.4
Protein
Docking
updated 8 days ago by
dthorbur
★ 1.7k • written 10 days ago by
Preeti
• 0
1
vote
5
replies
253
views
how to convert SummarizedExperiment files to DESeqDataSet??
scRNA-seq
DEG
DESeq2
updated 15 days ago by
Haci
▴ 550 • written 15 days ago by
kayah
• 0
1
vote
5
replies
374
views
Is there a reason why fastq files from SRAExplorer and SRAToolkit are different sizes?
sraexplorer
sratoolkit
updated 16 days ago by
GenoMax
140k • written 19 days ago by
biotrekker
▴ 100
2
votes
5
replies
606
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 14 days ago by
jkbonfield
★ 1.2k • written 14 days ago by
K
• 0
0
votes
5
replies
403
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
5 days ago by
Learner
• 0
2
votes
5
replies
2.3k
views
GTF file for HIV strain pNL4-3
HIV
annotation
mapping
updated 27 days ago by
xiaoleiusc
▴ 140 • written 5.8 years ago by
caggtaagtat
★ 1.8k
0
votes
4
replies
336
views
Dsuite Dinvestigate error but no indication as to the source
Dsuite
19 days ago by
Drew
• 0
3
votes
4
replies
425
views
Correlation for ATAC-Seq and Chip-Seq
RNA-Seq
Chip-Seq
ATAC-Seq
29 days ago by
qudrat.nii
▴ 10
0
votes
4
replies
355
views
Can I perform a Functional Enrichment Analysis on a specific list of pre-defined genes?
RNA-seq
DGE
11 days ago by
Adam
• 0
351 results • Page
1 of 8
Recent Votes
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: snippy error
Answer: TSS of protein coding genes
TSS of protein coding genes
Answer: vcf not indexing
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Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
ATpoint
81k
It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
Comment: Interproscan taking so much time
by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Ah, sorry, I was thinking of the wrong command. You can either use `seqtk sample` or `seqkit sample`. I would recommend the former if your …
Comment: Variant calling of GBS data
by
analyst
▴ 10
It does not output warning when I skip flags for MQRankSum and ReadPosRankSum **java -jar -Xmx30G gatk.jar VariantFiltration -R reference…
Comment: Merging featureCounts output for different species
by
andrebolerbarros
• 0
Is there any list of homology you could use for this merging? Maybe this would be helpful
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
again, remove the spaces " "SOR > 10." -> " "SOR>10"
Comment: Variant calling of GBS data
by
analyst
▴ 10
It is still giving same warning java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --fi…
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
dzisis1986
▴ 70
It doesn't make sense how to change the threads and in my case it is not working! What kind of problem is that ? is it related to Amazon to…
Comment: STAR aligner options
by
theophile
• 0
I have finally found out the reason behind this behavior. As [pointed out by dsull][1], the beginning of the alignment of read1 to the rat…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Right Pierre, thanks.
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
![enter image description here][1] [1]: /media/images/710829f2-e4af-4743-a31d-822520b4
Comment: Variant calling of GBS data
by
analyst
▴ 10
Vcf file contains this information ![enter image description here][1] [1]: /media/images/b3f699e5-2dd9-4e08-8f5b-2a716544
Comment: Variant calling of GBS data
by
analyst
▴ 10
Command used : **java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --filter-name "QD_f…
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