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181 results • Page
4 of 4
Sort: Rank
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Votes
Replies
1
vote
2
replies
242
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
5 days ago by
bioinfo
▴ 150
0
votes
3
replies
278
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 6 days ago by
noodle
▴ 580 • written 7 days ago by
doramora
▴ 10
0
votes
1
reply
152
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 6 days ago by
LauferVA
4.2k • written 7 days ago by
graeme.thorn
▴ 100
0
votes
2
replies
210
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
6 days ago by
melissa.joubert
• 0
1
vote
1
reply
152
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 6 days ago by
Ram
44k • written 7 days ago by
kilcdincer
▴ 10
1
vote
8
replies
484
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 3 days ago by
Alex Reynolds
35k • written 7 days ago by
ntsopoul
▴ 60
0
votes
2
replies
234
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
5 days ago by
Chen
• 0
0
votes
1
reply
137
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 6 days ago by
Ram
44k • written 7 days ago by
Emily
▴ 20
1
vote
3
replies
293
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 4 days ago by
GenoMax
142k • written 7 days ago by
ohtang7
▴ 40
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 6 days ago by
Ram
44k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
242
views
Help with IGV abbreviation
igv
updated 6 days ago by
Ram
44k • written 7 days ago by
GeneC
• 0
2
votes
5
replies
523
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 6 days ago by
Ram
44k • written 12 days ago by
Prawesh
• 0
2
votes
4
replies
314
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
6 days ago by
Esraa
• 0
1
vote
4
replies
362
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 6 days ago by
Juke34
8.6k • written 8 days ago by
Vijith
▴ 30
2
votes
6
replies
415
views
BWA alignment
Samtools
bam
updated 6 days ago by
a.alnawfal.1992
▴ 260 • written 8 days ago by
Vahid
• 0
0
votes
8
replies
532
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 1 day ago by
Pierre Lindenbaum
161k • written 10 days ago by
ajbarrett98
• 0
2
votes
9
replies
766
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 6 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
schmince
• 0
1
vote
4
replies
347
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 3 days ago by
Joe
21k • written 12 days ago by
cput
• 0
5
votes
7
replies
534
views
RNA seq analysis
DESeq
RNA-seq
6 days ago by
Jacek
▴ 20
0
votes
9
replies
671
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 6 days ago by
Wayne
★ 2.0k • written 14 days ago by
JACKY
▴ 140
1
vote
1
reply
193
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 4 days ago by
Jordan M Eizenga
▴ 460 • written 15 days ago by
sarumonsus
▴ 10
4
votes
10
replies
845
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 10 hours ago by
Alex Reynolds
35k • written 25 days ago by
J
▴ 10
0
votes
2
replies
303
views
Traveler with Infernal mapping failed
r2dt
updated 2 days ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
0
votes
9
replies
617
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
5 days ago by
Arton
▴ 10
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 1 day ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
19
votes
15
replies
2.3k
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 7 hours ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
6 days ago by
Arton
▴ 10
13
votes
17
replies
6.1k
views
9 follow
Blastn, need help to increase speed
RNA-Seq
blastn
blast+
updated 1 day ago by
m13113153781
• 0 • written 3.2 years ago by
chiachoong_leong93
▴ 20
1
vote
3
replies
809
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 4 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 3 days ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 4 days ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
181 results • Page
4 of 4
Recent Votes
Answer: converting transcript IDs (Ensembl) to gene symbols in R
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Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
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Recent Replies
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
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Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
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