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182 results • Page
4 of 4
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0
votes
2
replies
232
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
4 days ago by
analyst
▴ 50
0
votes
6
replies
421
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 4 days ago by
Ram
43k • written 7 days ago by
ajbarrett98
• 0
0
votes
11
replies
543
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
5 days ago by
Tuck898
• 0
2
votes
9
replies
696
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 10 days ago by
schmince
• 0
0
votes
5
replies
318
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 days ago by
SilhouetteQ
• 0
0
votes
2
replies
296
views
How are score_weights calculated in this code?
single-cell
6 days ago by
carolofharvest
▴ 40
0
votes
5
replies
331
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
4 days ago by
feather-W
• 0
1
vote
4
replies
341
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 4 days ago by
Ram
43k • written 9 days ago by
samRayne
• 0
0
votes
2
replies
231
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 9 days ago by
elisheva
▴ 120
5
votes
7
replies
491
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
Jacek
▴ 20
0
votes
9
replies
602
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 2 days ago by
Wayne
★ 2.0k • written 11 days ago by
JACKY
▴ 140
0
votes
4
replies
306
views
Correlation Analysis
statistics
methylation
NGS
expression
6 days ago by
Researcher
▴ 30
0
votes
1
reply
148
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 4 days ago by
Ram
43k • written 11 days ago by
David
• 0
1
vote
1
reply
184
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 1 day ago by
Jordan M Eizenga
▴ 460 • written 11 days ago by
sarumonsus
▴ 10
0
votes
3
replies
353
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
4 days ago by
mropri
▴ 150
3
votes
6
replies
489
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by
Pine
▴ 20 • written 12 days ago by
snajafy
• 0
0
votes
2
replies
297
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 14 days ago by
yahn
• 0
4
votes
7
replies
420
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
4 days ago by
Chen
• 0
3
votes
3
replies
268
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 4 days ago by
Ram
43k • written 17 days ago by
Adyasha
• 0
0
votes
7
replies
441
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 4 days ago by
Mohamed Abderrahmane
▴ 20 • written 18 days ago by
matteo.levorato
• 0
0
votes
0
replies
122
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 4 days ago by
Ram
43k • written 18 days ago by
atharvakarkare14
▴ 40
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
3 days ago by
Emily
▴ 20
2
votes
3
replies
276
views
Finding variants within a subset of a BAM file
variant
calling
3 days ago by
ramiro.barrantes
• 0
0
votes
9
replies
600
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
2 days ago by
Arton
▴ 10
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
6 days ago by
vytarasov
▴ 180
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
2 days ago by
Arton
▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 4 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
3
replies
797
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 1 day ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 4 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 4 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 9 hours ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 5 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
182 results • Page
4 of 4
Recent Votes
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Recent Replies
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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