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931 results • Page
4 of 19
Sort: Rank
Rank
Views
Votes
Replies
3
votes
5
replies
340
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
5 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 6 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
203
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
6 days ago by
dtnondorf
• 0
1
vote
7
replies
530
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 1 day ago by
Chris Dean
▴ 400 • written 6 days ago by
sovrappensiero
▴ 90
1
vote
2
replies
246
views
RNA-seq data for deep learning classification
rna-seq
6 days ago by
yahn
• 0
3
votes
8
replies
520
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
2 days ago by
Qroid
▴ 40
0
votes
1
reply
519
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 7 days ago by
Hugo
• 0 • written 5 months ago by
Rachel
• 0
0
votes
1
reply
158
views
Provean help
variant
Provean
updated 6 days ago by
Mensur Dlakic
★ 27k • written 7 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
168
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 7 days ago by
bk11
★ 2.4k • written 7 days ago by
Jeol
▴ 20
1
vote
1
reply
178
views
Super ehancers
enhancers
updated 7 days ago by
jared.andrews07
★ 16k • written 7 days ago by
Oburah
• 0
0
votes
6
replies
314
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 6 days ago by
dsull
★ 6.0k • written 7 days ago by
Chen
• 0
5
votes
5
replies
285
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 7 days ago by
atharvakarkare14
▴ 30 • written 7 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
457
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
6 days ago by
eebloom
▴ 80
3
votes
3
replies
337
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 6 days ago by
ATpoint
82k • written 7 days ago by
alifafiq1
• 0
0
votes
0
replies
102
views
Use of annotation of integrated Seurat object in single sample
Seurat
7 days ago by
Bine
▴ 60
0
votes
0
replies
108
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 7 days ago by
Ram
43k • written 7 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
231
views
Subsetting and merging back Seurat Object brings different results
Seurat
7 days ago by
Bine
▴ 60
0
votes
0
replies
155
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 7 days ago by
Ram
43k • written 7 days ago by
4r-rtg
• 0
1
vote
1
reply
145
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 7 days ago by
Ram
43k • written 7 days ago by
marco.barr
▴ 100
0
votes
0
replies
98
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
7 days ago by
Vijith
▴ 30
10
votes
14
replies
656
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 2 days ago by
GenoMax
142k • written 8 days ago by
nicole.kavanagh
• 0
0
votes
1
reply
284
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 7 days ago by
Scooter
▴ 280 • written 14 days ago by
avocado123
• 0
0
votes
0
replies
100
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
7 days ago by
James
▴ 10
0
votes
1
reply
590
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 7 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
247
views
Odd alignment question/finding
Alignment
updated 6 days ago by
barslmn
★ 2.1k • written 7 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
210
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 7 days ago by
GenoMax
142k • written 7 days ago by
mgranada3
▴ 30
0
votes
0
replies
102
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
7 days ago by
meck
• 0
0
votes
0
replies
128
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 7 days ago by
Ram
43k • written 7 days ago by
Oscar
▴ 10
0
votes
7
replies
573
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 6 days ago by
LChart
3.9k • written 10 days ago by
kl
▴ 10
0
votes
1
reply
228
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 7 days ago by
Adam
▴ 30 • written 8 days ago by
J
• 0
1
vote
3
replies
320
views
DESeq2 processing problems
deseq2
R
updated 7 days ago by
ATpoint
82k • written 8 days ago by
jagdish7921
• 0
0
votes
1
reply
786
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 7 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
155
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 7 days ago by
Ram
43k • written 8 days ago by
ernestine.kubi
• 0
0
votes
0
replies
108
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
8 days ago by
VITALA
• 0
1
vote
2
replies
263
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
7 days ago by
rianna.collins
• 0
0
votes
1
reply
195
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 8 days ago by
i.sudbery
19k • written 8 days ago by
Edmond
• 0
0
votes
0
replies
151
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
8 days ago by
O.rka
▴ 720
0
votes
1
reply
689
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 8 days ago by
Ram
43k • written 8 days ago by
Dr Huma Naz
• 0
2
votes
2
replies
285
views
p-value in CIBERSORT
CIBERSORT
p-value
8 days ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
390
views
Telescope issue
Telescope
RNA-seq
updated 8 days ago by
GenoMax
142k • written 8 days ago by
eleven11
• 0
5
votes
6
replies
543
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 9 days ago by
me
▴ 760 • written 10 days ago by
Mariana
▴ 40
1
vote
1
reply
240
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 8 days ago by
Ram
43k • written 9 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
299
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
8 days ago by
Nafi
• 0
1
vote
3
replies
297
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 8 days ago by
GenoMax
142k • written 9 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
292
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
3 days ago by
Dora
▴ 10
0
votes
0
replies
169
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 9 days ago by
Ram
43k • written 9 days ago by
Chakri
• 0
0
votes
2
replies
231
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
2 days ago by
Ahiad Chen Zion
• 0
1
vote
5
replies
345
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
6 days ago by
Riccardo
▴ 10
0
votes
0
replies
135
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 9 days ago by
Ram
43k • written 9 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
129
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 9 days ago by
Ram
43k • written 9 days ago by
Alexandros
• 0
931 results • Page
4 of 19
Recent Votes
Comment: WGCNA gene selection: gene significance or LASSO?
WGCNA gene selection: gene significance or LASSO?
Comment: absolute path for symbolic links in Snakefile
Answer: absolute path for symbolic links in Snakefile
A: Remove sequences <300 bases from FASTA file
Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
A: Insert Size And Fragment Size ?
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Scholar
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tim.booth
▴ 50
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to
strive
• 0
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LauferVA
4.2k
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ManuelDB
▴ 80
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nkls063408
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rj.rezwan
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Pierre Lindenbaum
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Recent Replies
Answer: Snakemake fails to find conda in PBS
by
tim.booth
▴ 50
Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile
by
tim.booth
▴ 50
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length
by
Pierre Lindenbaum
161k
I supect your reads are hard clipped. Show us the first lines of samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file
by
sainavyav22
• 0
Here you go. 1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput 2.perl annotate_variation.pl 100…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant. Your question is ambiguous because you…
Comment: Help with Biopython for Beginner
by
GenoMax
142k
> That turns it into a mess of paragraphs See above. Select (highlight with mouse) the part you want to represent as `code` and then click…
Comment: Help with Biopython for Beginner
by
cput
• 0
That turns it into a mess of paragraphs, but if it truly is more productive thanks for the tip!
Comment: Presence of unknown sites in ANNOVAR output file
by
Ram
43k
Please show us your full annovar command line.
Comment: input file for alternative splicing in rmats in linux
by
Ram
43k
I've done what I can to make your post more professional. Stick to outlining your problem, personal pleas do not really belong on a profess…
Comment: Contig assembly task, errors
by
rackbersingh
• 0
Hi Phillip, Thanks for providing an answer and clearing up some confusion, looking into what you said about older assemblers reverse comp…
Comment: How to analyze Infinium Mouse Methylation BeadChip array data?
by
Tawny
▴ 180
Did you get this figured out? I am having the same error in R.
Answer: JASPAR2024_getMatrixSet error
by
Raghad
• 0
Try this: ```r #Read the motifs library(JASPAR2024) library(TFBSTools) jaspar <- JASPAR2024() sq24 <- RSQLite::dbConnect(RSQLite::SQLite…
Answer: How to convert normalized BigWig file to count matrix?
by
ATpoint
82k
It's not possible. Gene counts are a region aggregate, bigwigs are a per-base readout and you cannot use normalized counts for mentioned to…
Comment: bcftools - reducing to "sites-only"?
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: bcftools - reducing to "sites-only"?
by
Matthew
• 0
Thank you Pierre! Not sure why I didn't notice that (I should have)
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