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607 results • Page
2 of 13
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2
votes
4
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823
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Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 2 days ago by
Ram
39k • written 3.6 years ago by
Christian
• 0
2
votes
0
replies
219
views
Reference request for getting the big picture of gene taxonomy
genes
textbook
19 days ago by
garbagelister
▴ 20
2
votes
2
replies
394
views
Online tool for creating figures of gene with its features
features
genes
figures
updated 19 days ago by
Ram
39k • written 6 months ago by
andre.arrudalima
▴ 20
2
votes
5
replies
390
views
RNA SEQ reads assembly for illumina sequenced data
NGS
linux
nanopore
updated 28 days ago by
Ram
39k • written 5 weeks ago by
Adyasha
• 0
2
votes
3
replies
228
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 1 day ago by
GenoMax
130k • written 1 day ago by
ev97
• 0
2
votes
4
replies
1.3k
views
hisat2 SyntaxError: invalid syntax
alignment
hisat2
updated 23 days ago by
Ram
39k • written 19 months ago by
Xiaoyun
▴ 10
2
votes
3
replies
342
views
Low mapping percentage
mapping
STAR
RNAseq
4 days ago by
Sib
▴ 40
2
votes
1
reply
1.8k
views
How do I apply a patch to hg38?
reference
human
freeze
hg38
patch
updated 6 days ago by
Jeremy Leipzig
21k • written 5.6 years ago by
imperialcommando117
• 0
2
votes
3
replies
372
views
What's your recommended length and depth for my RNA-seq experiment
RNA-seq
updated 21 days ago by
rfran010
▴ 170 • written 4 weeks ago by
biotech&Analytics
▴ 10
2
votes
7
replies
1.5k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence
ncbi
gene
genbank
updated 16 days ago by
Ram
39k • written 5.3 years ago by
navela78
▴ 70
2
votes
1
reply
200
views
'Seurat' package
Seurat
R
updated 27 days ago by
Ram
39k • written 27 days ago by
sooni
• 0
2
votes
1
reply
269
views
scRNAseq (bioconductor) data to seurat object
bioconductor
seurat
scRNAseq
updated 20 days ago by
ATpoint
72k • written 20 days ago by
Alex
▴ 20
2
votes
0
replies
724
views
Why are there multiple bax/fastq files associated with my PacBio run?
genome
PacBio
WGS
sequencing
updated 8 days ago by
Ram
39k • written 4.1 years ago by
nickvpinkham
▴ 20
2
votes
2
replies
770
views
LOG2FCs representation
LOG2FC
DESeq2
PCR
updated 23 days ago by
Ram
39k • written 17 months ago by
Akash D
▴ 40
2
votes
2
replies
119
views
how to use Hemtools bed2vcf?
vcf
linux
conversion
bed
updated 8 days ago by
Pierre Lindenbaum
154k • written 8 days ago by
MobiusT
▴ 10
2
votes
4
replies
239
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 7 days ago by
Ram
39k • written 7 days ago by
miguellarrazlopezdenovales
• 0
2
votes
5
replies
418
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
8 days ago by
DanielEB_fisk
▴ 10
2
votes
1
reply
203
views
P values on box plots
sequencing
Statistics
RNA
updated 27 days ago by
Basti
★ 1.6k • written 27 days ago by
Abdullah
▴ 10
2
votes
3
replies
278
views
Using RNA-seq to detect pathogen sequences in host tissue
RNA-seq
14 days ago by
erik.burchard
▴ 10
2
votes
0
replies
798
views
how to find the bound form of an enzyme structure?
enzyme
updated 26 days ago by
Ram
39k • written 6.0 years ago by
lochanamp
▴ 70
2
votes
6
replies
1.0k
views
Time series RNA seq design query
RNA-seq
time-series
deseq2
updated 8 days ago by
Ram
39k • written 18 months ago by
kra277
• 0
2
votes
6
replies
387
views
Find data-based Gene_IDs for unknown gene_IDs in gtf.file
RNA-SEQ
annotation
GO-term
17 days ago by
Pegasus
▴ 90
2
votes
6
replies
646
views
How to identify the corresponding gene of a short sequence of a genome?
fasta
gene
genome
sequence
updated 1 day ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
2
votes
3
replies
1.2k
views
mutational signatures in different tumor samples
somatic mutation
mutational signature
updated 6 days ago by
Vincent Laufer
★ 2.9k • written 4.4 years ago by
lzy
▴ 20
2
votes
2
replies
771
views
Final year project query
project
updated 13 days ago by
Ram
39k • written 4.5 years ago by
talhar123456
• 0
2
votes
3
replies
343
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
28 days ago by
Dan
▴ 120
2
votes
3
replies
863
views
Freebayes command stopped due to lack of space
freebayes
SNP-calling
updated 14 days ago by
Ram
39k • written 5.0 years ago by
amcheroo
• 0
2
votes
8
replies
2.6k
views
How to convert a database from protein to nucleotide
blastn
unix
blastx
blast
updated 27 days ago by
Ram
39k • written 6.2 years ago by
AJTrunkskun94
• 0
2
votes
5
replies
444
views
How to check a gene in an open chromatin region or not?
ATAC-seq
29 days ago by
Chris
▴ 100
2
votes
3
replies
381
views
Samtools faidx can't be run in succession on two reference files?
Samtools
25 days ago by
DdogBoss
• 0
2
votes
2
replies
308
views
DESeq factor order
DESeq2
20 days ago by
Chris
▴ 10
2
votes
3
replies
690
views
Including bioinformatics into an agriculture/horticulture dissertation project
agrobioinformatics
plant-gene-analysis
updated 8 days ago by
Ram
39k • written 4.1 years ago by
cipri91rusu
• 0
2
votes
3
replies
110
views
[Waiting on OP] perl script to grep a part of header from fasta seq file
perl
updated 20 days ago by
Ram
39k • written 5.4 years ago by
h_asma
• 0
1
vote
3
replies
621
views
miRDeep2.pl error in make_html2.pl
miRNA
mirDeep
make_html2.pl
updated 23 days ago by
Ram
39k • written 21 months ago by
tikshyadav19
• 0
1
vote
3
replies
134
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence
genome
prediction
masking
updated 10 hours ago by
Darked89
4.4k • written 13 hours ago by
Ayish
• 0
1
vote
0
replies
97
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
6 days ago by
Jonathan Lefebre
▴ 70
1
vote
3
replies
194
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 6 days ago by
Pierre Lindenbaum
154k • written 7 days ago by
herh
• 0
1
vote
2
replies
209
views
Combination of ROC CURVE
roccurve
R
AUC
3 days ago by
Maria17
▴ 20
1
vote
0
replies
940
views
can the differences in the protein sequence be ranked according to their relevance to a certain stimuli, using a statistical method when the protein …
sequence
proteins
updated 23 days ago by
Ram
39k • written 5.9 years ago by
lochanamp
▴ 70
1
vote
3
replies
999
views
BLAST: overflow error
BLAST
updated 26 days ago by
Ram
39k • written 13 months ago by
antoinefelden
▴ 50
1
vote
1
reply
1.6k
views
Bioinformatics tools for Plasmid detection
short-read
plasmid
updated 6 days ago by
Ram
39k • written 3.9 years ago by
El Niño
▴ 10
1
vote
3
replies
188
views
Obtain a --gene-trans-map file after rnaSPAdes
rnaSPAdes
Trinity
2 days ago by
UserA
• 0
1
vote
1
reply
2.6k
views
Comparing time series expression data
time-series
gene-expression
updated 8 days ago by
Ram
39k • written 5.8 years ago by
The
▴ 180
1
vote
3
replies
1.4k
views
How to check quality of multiple sequence alignment (MSA)?
MSA
multiple-sequence-alignment
R
updated 22 days ago by
Ram
39k • written 3.2 years ago by
Chirag Parsania
★ 2.0k
1
vote
1
reply
517
views
Seqrecord object to only a single line sequence (without ID)
SeqIO
biopython
python
updated 26 days ago by
Ram
39k • written 2.1 years ago by
voltosj
• 0
1
vote
1
reply
277
views
How do I use the new human pangenome reference to discover SNV and SV.
pangenome
reference
graph
vg
27 days ago by
Pierre Lindenbaum
154k
1
vote
3
replies
227
views
Differential protein expression analysis
R
proteomic
statistics
updated 11 hours ago by
dsull
★ 4.2k • written 4 days ago by
Ribo
▴ 40
1
vote
3
replies
439
views
Need help in using dada2
dada2
R
updated 26 days ago by
Ram
39k • written 8 months ago by
rishav513
▴ 30
1
vote
2
replies
1.4k
views
Getting full list for DEGs in Noiseq
RNA-Seq
updated 20 days ago by
Ram
39k • written 5.4 years ago by
mubangafchama
▴ 10
1
vote
2
replies
239
views
`MOFAobject@expectations` is empty list
MOFA2
updated 28 days ago by
Ram
39k • written 28 days ago by
Dan
▴ 120
607 results • Page
2 of 13
Recent Votes
NM_transcript ID gene identification
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
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Comment: pal2nal -nogap -nomismatch options not working
by
Marie
• 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag
by
Pierre Lindenbaum
154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Ram
39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag
by
Ram
39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Arup Ghosh
3.2k
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