Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
185 results • Page
1 of 4
Sort: Views
Rank
Views
Votes
Replies
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 6 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
5 days ago by
vytarasov
▴ 180
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
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 3 days ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 6 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
4
votes
5
replies
4.3k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 12 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 3 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
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
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 2 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 1 day ago by
Ram
43k • written 3.9 years ago by
millere
• 0
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 3 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
3
replies
795
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 17 hours ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
5
replies
786
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
2
votes
9
replies
694
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
schmince
• 0
2
votes
11
replies
620
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
4 hours ago by
egascon
• 0
1
vote
14
replies
602
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
6 hours ago by
hophuquy0944
• 0
0
votes
9
replies
598
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
1 day ago by
Arton
▴ 10
0
votes
9
replies
597
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 1 day ago by
Wayne
★ 2.0k • written 10 days ago by
JACKY
▴ 140
2
votes
5
replies
567
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 4 days ago by
arctic
▴ 40 • written 13 days ago by
M.
▴ 30
0
votes
1
reply
545
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 1 day ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
11
replies
533
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
4 days ago by
Tuck898
• 0
0
votes
1
reply
533
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 4 days ago by
aw7
▴ 300 • written 27 days ago by
abhishekghadge
• 0
1
vote
4
replies
499
views
cellranger error message
multiplexing
cellranger
updated 6 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
2
votes
5
replies
491
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 2 days ago by
Ram
43k • written 8 days ago by
Prawesh
• 0
3
votes
6
replies
489
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 4 days ago by
Pine
▴ 20 • written 11 days ago by
snajafy
• 0
5
votes
7
replies
485
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
Jacek
▴ 20
1
vote
3
replies
432
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
3 days ago by
kalavattam
▴ 190
0
votes
7
replies
428
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
2
replies
425
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
3 days ago by
David Langenberger
11k
0
votes
6
replies
419
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 3 days ago by
Ram
43k • written 6 days ago by
ajbarrett98
• 0
1
vote
4
replies
412
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
GenoMax
142k • written 29 days ago by
aniigodwinn
• 0
4
votes
7
replies
408
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
3 days ago by
Chen
• 0
0
votes
4
replies
397
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 0
1
vote
9
replies
393
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 6 days ago by
i.sudbery
19k • written 10 days ago by
Assa Yeroslaviz
★ 1.8k
6
votes
7
replies
385
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
4 days ago by
sansan_96
▴ 90
2
votes
6
replies
380
views
BWA alignment
Samtools
bam
updated 2 days ago by
a.alnawfal.1992
▴ 260 • written 4 days ago by
Vahid
• 0
1
vote
7
replies
380
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
2 days ago by
ntsopoul
▴ 60
2
votes
8
replies
377
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
Matteo Ungaro
▴ 100
3
votes
3
replies
359
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 3 days ago by
Mathew
▴ 140 • written 6 days ago by
Christopher
• 0
1
vote
2
replies
358
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 3 days ago by
Ram
43k • written 4 days ago by
t.fortunato.asquini
• 0
0
votes
3
replies
352
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
3 days ago by
mropri
▴ 150
1
vote
4
replies
343
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 3 days ago by
Vijith
▴ 30
0
votes
9
replies
342
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
1 day ago by
njornet
▴ 20
0
votes
3
replies
342
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
1
vote
4
replies
339
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 3 days ago by
Ram
43k • written 8 days ago by
samRayne
• 0
3
votes
4
replies
335
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
Pierre Lindenbaum
161k
0
votes
5
replies
330
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
4 days ago by
feather-W
• 0
185 results • Page
1 of 4
Recent Votes
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Recent Locations •
All
Spain,
just now
South Korea,
just now
Bologna,
1 minute ago
India,
2 minutes ago
Budapest,
3 minutes ago
Belgium,
4 minutes ago
Lebanon,
4 minutes ago
Recent Awards •
All
Popular Question
to
ashkan
▴ 160
Supporter
to
Umer
▴ 50
Scholar
to
zx8754
11k
Teacher
to
Rob
6.6k
Popular Question
to
Nyksubuz
▴ 20
Popular Question
to
Govardhan Anande
▴ 150
Popular Question
to
Lhl
▴ 760
Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Traffic: 2174 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6