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122,217 results • Page
718 of 2445
Sort: Rank
Rank
Views
Votes
Replies
0
votes
7
replies
7.8k
views
Phasing vcf file with Beagle
vcf
phasing
beagle
haplotype
bash
updated 4.5 years ago by
明梓
• 0 • written 4.8 years ago by
sixthirty
• 0
1
vote
1
reply
983
views
Genomic Variant calling from RNA-Seq Data
RNA-Seq
SNP
Genomic
Variant
updated 4.8 years ago by
Kevin Blighe
★ 90k • written 4.8 years ago by
hkarakurt
▴ 200
7
votes
18
replies
7.3k
views
problem in matching the names between file names and patients Id in TCGA
TCGA
CNV
problem in matching
updated 4.8 years ago by
HB
▴ 30 • written 7.5 years ago by
nazaninhoseinkhan
▴ 530
0
votes
3
replies
1.0k
views
Estrogen hormonal signalling genes
RNA-Seq
4.8 years ago by
glady
▴ 320
0
votes
0
replies
622
views
How to find fixed mutations between populations
fixed mutations
4.8 years ago by
Yongjie Zhang
▴ 110
6
votes
13
replies
2.5k
views
Blast in parallel with edible outfmt
blast
output
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
K.Gee
▴ 40
2
votes
8
replies
2.3k
views
HDF5-DIAG: Error in using dsk
GATB
updated 4.8 years ago by
claire.lemaitre
▴ 120 • written 4.8 years ago by
manozawa439
• 0
2
votes
4
replies
1.6k
views
Two Sample t-test with bootstrapping for gene expression matrix in R
RNA-Seq
R
updated 4.8 years ago by
e.rempel
★ 1.1k • written 4.8 years ago by
Expert
▴ 10
1
vote
1
reply
1.1k
views
Does transcriptome assembly data contains introns?
Transcriptome
RNA-Seq
Stringtie
Hisat2
Assembly
updated 4.8 years ago by
lieven.sterck
16k • written 4.8 years ago by
noorussubah95
▴ 20
0
votes
0
replies
864
views
Tools for structural variant on exome
exome
sequencing
SV
structural variant
4.8 years ago by
quentin54520
▴ 120
1
vote
1
reply
3.3k
views
Samtools Mpileup Doesn'T Show Deletion, When Deletion Between Paddings
samtools
mpileup
bam
ngs
updated 4.8 years ago by
aroob.lab
• 0 • written 12.7 years ago by
tsk
▴ 10
8
votes
22
replies
16k
views
Creating reference Index using Bowtie2
genome
alignment
next-gen
Assembly
updated 4.1 years ago by
Ram
45k • written 11.4 years ago by
cvu
▴ 180
2
votes
6
replies
1.7k
views
change the header of fasta sequence
fasta
name
written 4.8 years ago by
harry
▴ 40
0
votes
0
replies
597
views
Are there any databases for gene co-expression or gene clustering by spatial/cell-type patterns?
rna-seq
gene
4.8 years ago by
Yep
▴ 20
0
votes
0
replies
709
views
Probability of rare variants
variants
statistics
probability
4.8 years ago by
Genomics
▴ 20
1
vote
0
replies
655
views
Multifactor analysis in DESeq2
RNA-Seq
4.8 years ago by
a.basitkhan1990
▴ 60
0
votes
2
replies
1.3k
views
Stacks 1.44 Error
RAD-Seq
ddRAD
Stacks
updated 4.8 years ago by
h.mon
35k • written 4.8 years ago by
virtualinterlect
• 0
5
votes
4
replies
6.6k
views
How to download multiple fasta files from NCBI in linux command line?
fasta
linux
command line
NCBI
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
Anisur Rahman
▴ 80
2
votes
18
replies
4.0k
views
Uploaded bam file into IGV but couldn't see anything
alignment
4.8 years ago by
dreamfeathers08
▴ 10
0
votes
2
replies
1.6k
views
bigWig tracks inconsistent with MACS2 callpeak
ChIP-Seq
MACS2
4.8 years ago by
lida
▴ 10
3
votes
6
replies
4.0k
views
Problem using PicardTools MarkDuplicates: SortingCollection: There is not enough memory per file for buffering. Reading will be unbuffered.
genome
updated 4.8 years ago by
Medhat
9.8k • written 4.8 years ago by
pengxw1990
• 0
0
votes
0
replies
954
views
Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?
short reads
Illumina
barcodes removal
FLEXBAR
4.8 years ago by
giulia.trauzzi
▴ 30
0
votes
1
reply
1.3k
views
Structural variations intersection
next-gen
SNP
updated 4.8 years ago by
Biostar
20 • written 4.9 years ago by
tomilova.ekaterina.rp
• 0
1
vote
0
replies
2.9k
views
Merging subsets in Seurat after SCTransform
seurat
subset
sctransform
merge
DEGs
4.8 years ago by
VolEr
▴ 40
0
votes
0
replies
778
views
Missing S:N501Y from Clade 20H/501Y.V2 identified by Nextclade
Nextclade
4.8 years ago by
arash.iranzadeh1980
▴ 30
3
votes
6
replies
3.6k
views
User-defined coverage in CollectHsMetrics [Picard]
next-gen
picard
coverage
broadinstitute
updated 4.8 years ago by
sh001
• 0 • written 8.4 years ago by
anu014
▴ 190
3
votes
14
replies
3.9k
views
Samtools depth to get the read depth
sequencing
RNA-Seq
4.8 years ago by
bandanaschapagain
▴ 40
4
votes
4
replies
7.4k
views
How to get real cell names from Seurat Object?
rna-seq
updated 4.8 years ago by
from the mountains
▴ 250 • written 4.8 years ago by
leranwangcs
▴ 150
0
votes
0
replies
867
views
Is there a way to identify which MSTRGs (novel StringTie transcripts) are potential novel ncRNAs?
MSTRG
RNAseq
StringTIe
ncRNA
Novel Transcripts
4.8 years ago by
Jen
▴ 100
7
votes
23
replies
9.5k
views
Batch download genome feature file by RefSeq
gbff
ncbi
refseq
4.8 years ago by
ben83
▴ 50
3
votes
3
replies
4.9k
views
How to download a list of all KEGG orthologs with respect to KEGG module (or pathway) in Python?
kegg
database
python
updated 3.3 years ago by
Alexander
• 0 • written 4.8 years ago by
O.rka
▴ 750
3
votes
2
replies
1.9k
views
How to check for completeness of a mitochondrial or chloroplast genome?
genome-completeness
organelles
updated 2.2 years ago by
Ram
45k • written 4.8 years ago by
kristina.mahan
▴ 180
0
votes
2
replies
2.0k
views
minimap2 alignment for maker
maker
minimap2
annotation
alignment
4.8 years ago by
gilsorek12
▴ 10
0
votes
0
replies
723
views
How can I analyze a VCF dataset without an annotated reference genome
RNA-Seq
R
genome
gatk
galaxy
4.8 years ago by
julianneradford
▴ 20
2
votes
6
replies
5.0k
views
convert DNA FASTA file to RNA FASTA file
RNA-Seq
ChIP-Seq
sequence
updated 4.8 years ago by
JC
13k • written 4.8 years ago by
xiaoleiusc
▴ 140
0
votes
0
replies
631
views
Centrifuge (Classifier for metagenomic sequences)
software error
4.8 years ago by
amanpruthi15
• 0
0
votes
3
replies
2.2k
views
How can I run "gene set enrichment" (not necessarily GSEA) with only one condition?
metagenomics
gene set enrichment
analysis
GSEA
4.8 years ago by
O.rka
▴ 750
0
votes
0
replies
685
views
smallRNA-seq alignment with bowtie1:what is the argument for handling multi-mapped reads?
alignment
smallRNA-seq
bowtie1
multi-mapped reads
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
ooluwayiose
• 0
1
vote
1
reply
1.7k
views
tsv file genome coverage
tsv
genome
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
kimkes25
▴ 50
0
votes
8
replies
2.0k
views
Finding suboptimal alignments
sequencing
DNA
alignment
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
trinityduke100
▴ 10
13
votes
11
replies
6.5k
views
8 follow
Visualization of protein structure in R (Shiny)
R
rshiny
pdb
protein structure
visualization
updated 4.7 years ago by
n.s.j.vandervelden
▴ 90 • written 5.2 years ago by
aquaq
▴ 40
0
votes
1
reply
2.4k
views
Convert .sqn file to .gbk
organelle
updated 2.2 years ago by
Ram
45k • written 4.8 years ago by
kristina.mahan
▴ 180
1
vote
3
replies
2.6k
views
PCA with PLINK and SmartPCA: same imput file but different results in my plot. Why?
PCA
PLINK
smartPCA
EIGENSTRAT
plot
4.8 years ago by
francesca94.minnai
• 0
3
votes
1
reply
1.8k
views
Tool for extracting copy number alterations from a .maf mutation file
cna
maf
updated 4.8 years ago by
Kevin Blighe
★ 90k • written 4.8 years ago by
genomics Newbie
▴ 90
1
vote
4
replies
1.8k
views
Change sample order in plotHeatmap?
deepTools
plotHeatmap
computeMatrix
updated 3.3 years ago by
Alice Laigle
• 0 • written 4.8 years ago by
konsta.kukkonen
• 0
3
votes
5
replies
3.3k
views
Clustering sequences with low identity
clustering
sequences
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
agata88
▴ 870
0
votes
1
reply
831
views
ICGC data download
ICGC
local server
4.8 years ago by
Zahra
▴ 110
0
votes
1
reply
841
views
how to make BBmerge produce same strand fastq file
BBmerge
4.8 years ago by
shangguandong1996
▴ 30
3
votes
5
replies
2.2k
views
Newbie CIGAR question
SNP
alignment
sequence
updated 4.8 years ago by
Biostar
20 • written 9.1 years ago by
michael
• 0
1
vote
0
replies
1.4k
views
How to get RSIDs of indels from GWAS summary statistics
R
gene
snp
4.8 years ago by
Fede_Santos95
▴ 20
122,217 results • Page
718 of 2445
Recent Votes
Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
Comment: Question about QC and scrublet
by
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3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms?
by
lieven.sterck
16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
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by
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@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
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colindaven
8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated?
by
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8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated?
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154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
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by
Matteo Ungaro
▴ 140
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind
by
ATpoint
90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read
by
cmdcolin
★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
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Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
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