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510 results • Page
1 of 11
Sort: replies
Rank
Views
Votes
Replies
0
votes
16
replies
3.2k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 7 days ago by
Ram
39k • written 5.0 years ago by
rororo
• 0
3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 6 hours ago by
Ram
39k • written 4.2 years ago by
Star
▴ 60
1
vote
14
replies
2.8k
views
How to convert Haplotypes file to PLINK format data
R
plink
updated 7 days ago by
Ram
39k • written 5.0 years ago by
bha
▴ 80
7
votes
12
replies
840
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 5 days ago by
Sasha
▴ 180 • written 12 days ago by
Chris
▴ 100
0
votes
12
replies
2.9k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 13 days ago by
Ram
39k • written 5.6 years ago by
fonteneaudam
▴ 20
6
votes
12
replies
561
views
Help with error in cellranger
Cellranger
updated 13 days ago by
GenoMax
129k • written 14 days ago by
Chris
▴ 100
5
votes
10
replies
412
views
Error when viewing a bam file
samtools
29 days ago by
Chris
▴ 100
1
vote
10
replies
2.5k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 4 days ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
6
votes
9
replies
929
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM
Bowtie
updated 19 days ago by
Ram
39k • written 4 months ago by
luzglongoria
▴ 40
3
votes
9
replies
503
views
Estimate sizes of repeats in a especific Gene
CGG
Fragile-X
13 days ago by
Rafael
▴ 10
1
vote
9
replies
516
views
gene annotation
gtf
gene-annotation
updated 18 days ago by
Ram
39k • written 18 days ago by
ahmad
• 0
1
vote
9
replies
827
views
Couldn't get a file descriptor referring to the console multiqc
multiqc
updated 18 days ago by
Ram
39k • written 11 months ago by
smithkthedale
▴ 10
1
vote
8
replies
855
views
Betacoronavirus.00.nsq error
corona
biostars
updated 15 days ago by
Ram
39k • written 16 months ago by
Sam
• 0
2
votes
8
replies
2.6k
views
How to convert a database from protein to nucleotide
blastn
unix
blastx
blast
updated 19 days ago by
Ram
39k • written 6.2 years ago by
AJTrunkskun94
• 0
1
vote
8
replies
513
views
snpeff install error
snpeff
updated 19 days ago by
Ram
39k • written 4 weeks ago by
bestone
▴ 10
4
votes
8
replies
514
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
7 days ago by
eesha28112001
• 0
3
votes
8
replies
1.7k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 5 days ago by
Ram
39k • written 4.6 years ago by
nagendranp1991
• 0
3
votes
8
replies
1.3k
views
Kallisto mapping paired end
Kallisto
mapping
updated 18 days ago by
Ram
39k • written 15 months ago by
Dk
▴ 20
7
votes
7
replies
4.3k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 6 hours ago by
Ram
39k • written 4.4 years ago by
stu111538
▴ 80
5
votes
7
replies
643
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq
sequencing
updated 9 days ago by
supernovamik
• 0 • written 3.4 years ago by
ee.mohseni.alert
▴ 50
2
votes
7
replies
1.5k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence
ncbi
gene
genbank
updated 8 days ago by
Ram
39k • written 5.2 years ago by
navela78
▴ 70
0
votes
7
replies
2.2k
views
How much time should be expected for building a database by kraken2-build?
kraken2
updated 18 days ago by
Ram
39k • written 2.3 years ago by
thitrucminh.nguyen
• 0
3
votes
7
replies
1.6k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance
RNA-SEQ
RSEM
Trinity
updated 15 days ago by
Ram
39k • written 20 months ago by
Princy
▴ 60
0
votes
7
replies
570
views
fasterq-dump outputs "Cannot use '--ngc' as ngc file."
sra-tools
SRA
command-line
wrapper
updated 24 days ago by
ATpoint
72k • written 26 days ago by
gernophil
▴ 10
1
vote
7
replies
5.6k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 14 hours ago by
dare_devil
★ 3.1k • written 5.3 years ago by
win
▴ 940
6
votes
7
replies
1.4k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters
Algorithm
Software
updated 18 days ago by
Ram
39k • written 6.0 years ago by
nilo
▴ 90
5
votes
7
replies
878
views
error while using cyvcf2 to parse the vcf file
cyvcf2
vcf
htslib
updated 18 days ago by
Ram
39k • written 12 months ago by
rheab1230
▴ 140
0
votes
7
replies
567
views
How to test DEGs from microarray data on RNA-seq dataset
microarray
differential
limma
RNA-seq
expression
prediction
25 days ago by
Llander
• 0
1
vote
7
replies
867
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto
STAR
RNA-seq
Transcript_variants
13 days ago by
sohail.mbio
• 0
2
votes
6
replies
363
views
Find data-based Gene_IDs for unknown gene_IDs in gtf.file
RNA-SEQ
annotation
GO-term
9 days ago by
Pegasus
▴ 90
1
vote
6
replies
564
views
DESeq2
heatmap
R
DESeq2
21 days ago by
Nelo
• 0
2
votes
6
replies
532
views
how to make a venn plot with data frame in R
plot
R
Venn
9 days ago by
satva72
• 0
4
votes
6
replies
418
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
13 days ago by
natalev
▴ 20
0
votes
6
replies
215
views
how to create correlation matrix R
pearson-correlation
R
updated 7 hours ago by
GenoMax
129k • written 13 hours ago by
satva72
• 0
1
vote
6
replies
775
views
Trimmomatic FileNotFoundException
trimmomatic
updated 18 days ago by
Ram
39k • written 10 months ago by
awhale01
• 0
3
votes
6
replies
538
views
Convert Nanopore Fast5 files to Fasta format
fast5
fasta
Nanopore
6 days ago by
Sowmya Pulapet
▴ 30
0
votes
6
replies
1.0k
views
How do I tell piRNA population suppress TEs in a bed file?
mapping
piRNAs
TEs
updated 6 days ago by
Ram
39k • written 4.8 years ago by
jaqx008
▴ 110
0
votes
6
replies
320
views
Demultiplexing bam file
demultiplexing
bam_file
Iontorrent
1 day ago by
hasani.iut6
▴ 60
2
votes
6
replies
999
views
Time series RNA seq design query
RNA-seq
time-series
deseq2
updated 8 hours ago by
Ram
39k • written 18 months ago by
kra277
• 0
0
votes
6
replies
646
views
Comparative transcriptomics
rna-seq
comparative
transcriptomics
updated 12 days ago by
Vincent Laufer
★ 2.8k • written 12 months ago by
edus_bioinfo
▴ 20
3
votes
6
replies
1.8k
views
Biopython TimeExceptionError how to handle?
biopython
entrez
updated 13 days ago by
Ram
39k • written 5.6 years ago by
Xylanaser
▴ 80
3
votes
6
replies
1.1k
views
how to get total read count, mapped read count and unmapped read count from multiple sam or bam files
RNAseq
PYTHON
R
bash
updated 14 days ago by
Ram
39k • written 2.7 years ago by
Bioinfonext
▴ 430
4
votes
6
replies
739
views
Open-Source software. Good or bad for the market?
genomic-analysis
software
updated 11 days ago by
Ram
39k • written 5.2 years ago by
Bioinformatician90
• 0
0
votes
6
replies
552
views
Heatmap error: 'x' must be a numeric matrix
Heatmap
updated 18 days ago by
Ram
39k • written 16 months ago by
adnan.sabar7865
▴ 20
6
votes
6
replies
540
views
On "wings" in volcano plots...
DEG
volcano
DGE
statistics
DE
updated 11 days ago by
ATpoint
72k • written 12 days ago by
kalavattam
▴ 120
0
votes
6
replies
609
views
Getting Error when trying to run hisat2 script! Please help!
hisat2
updated 18 days ago by
Ram
39k • written 11 months ago by
smithkthedale
▴ 10
4
votes
6
replies
522
views
How to pass from DNA to AA fasta
genetics
updated 8 days ago by
Buffo
★ 2.2k • written 11 days ago by
Anderson Stiward
• 0
6
votes
6
replies
2.6k
views
ChIP-Seq Intensity Analysis
R
ChIP-Seq
updated 13 days ago by
Ram
39k • written 5.5 years ago by
solveforj
▴ 20
0
votes
5
replies
804
views
Read DNA sequence from FASTA rising a subclass?
FASTA
python
updated 11 days ago by
Ram
39k • written 2.6 years ago by
Gonçalo
• 0
2
votes
5
replies
438
views
How to check a gene in an open chromatin region or not?
ATAC-seq
21 days ago by
Chris
▴ 100
510 results • Page
1 of 11
Recent Votes
Answer: How do you add an ORF that overlaps the two regions where a circular genome is c
C: PLINK logistic regression analysis and covariates
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
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tarek.mohamed
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★ 2.3k
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Recent Replies
Comment: Unusual FASTQ file
by
Ram
39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ?
by
bhumm
▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file
by
bhumm
▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline
by
ATpoint
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
by
swbarnes2
13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline
by
Ram
39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline
by
Ram
39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree
by
GenoMax
129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline
by
Ram
39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
by
ashleymb1116
• 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index
by
GenoMax
129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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