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1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
0
votes
16
replies
3.8k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 11 months ago by
Ram
43k • written 5.9 years ago by
rororo
▴ 10
0
votes
7
replies
3.8k
views
MUMmer plot visualization
MUMmer plot
updated 9 weeks ago by
Carlos
• 0 • written 3.2 years ago by
rthapa
▴ 90
2
votes
4
replies
3.7k
views
Converting different annotation file formats (GTF/GFF/BED) to each other
rna-seq
next-gen
updated 6 months ago by
alejandrogzi
▴ 120 • written 6.6 years ago by
Javad
▴ 150
2
votes
4
replies
3.7k
views
6 follow
Gene correlation with single cell data?
RNA-Seq
gene
updated 3 months ago by
Quang
• 0 • written 3.1 years ago by
theodore.killian
▴ 30
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Pranavathiyani G
▴ 330
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 15 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
5
votes
35
replies
3.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 10 months ago by
anivlete
• 0
1
vote
2
replies
3.5k
views
rna-seq analysis with Salmon - how to Import and summarize using tximport
RNA-Seq
salmon
tximport
updated 6 months ago by
camillab.
▴ 160 • written 4.7 years ago by
woojoy14
▴ 10
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 29 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
0
votes
2
replies
3.5k
views
dN/dS ratio from .vcf file
synonmous
non-synomous
mutation
updated 6 months ago by
rohitsatyam102
▴ 840 • written 5.4 years ago by
shubhra.bhattacharya
▴ 140
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan
SNP
updated 10 months ago by
Ram
43k • written 9.5 years ago by
zhaojianli198322
• 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 7 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
3
votes
4
replies
3.4k
views
Switch ref/alt alleles vcf file
SNP
vcf
sequencing
updated 3 months ago by
jvt
• 0 • written 4.4 years ago by
mdstep
▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 8 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
1
vote
2
replies
3.4k
views
How to convert FASTA to NEXUS in Python
fasta
biopython
nexus
updated 9 months ago by
Ram
43k • written 3.7 years ago by
adrian18_07
▴ 10
0
votes
4
replies
3.4k
views
Polyploidy found, and not supported by vcftools
SNP
updated 10 months ago by
Ram
43k • written 5.2 years ago by
sambioinfo2018
▴ 20
1
vote
1
reply
3.4k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 10 months ago by
sackettl
▴ 20 • written 7.8 years ago by
maria.segovia.ramirez
▴ 10
0
votes
0
replies
3.4k
views
Find conserved blocks and extract subalignment with Python
multiple-sequence-alignment
python
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Kevin D
▴ 30
1
vote
14
replies
3.3k
views
How to convert Haplotypes file to PLINK format data
R
plink
updated 11 months ago by
Ram
43k • written 5.9 years ago by
bha
▴ 80
2
votes
12
replies
3.3k
views
WCGNA installation help
R
WGCNA
updated 11 weeks ago by
Ram
43k • written 4.9 years ago by
prekrish
• 0
1
vote
6
replies
3.3k
views
Filter VCF file
snp
next-gen
updated 10 months ago by
Ram
43k • written 7.8 years ago by
sukesh1411
▴ 30
0
votes
12
replies
3.3k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 11 months ago by
Ram
43k • written 6.5 years ago by
fonteneaudam
▴ 20
1
vote
9
replies
3.3k
views
build databses for genome using snpEff
annotation
SNP
snpEff
updated 8 months ago by
nehakhilwani18
• 0 • written 5.7 years ago by
StudentBio
• 0
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 11 months ago by
Ram
43k • written 3.1 years ago by
roybatty269
• 0
2
votes
5
replies
3.3k
views
How to output colored alignment from clustal omega stand alone tool?
Clustal Omega
Colored alignment
updated 8 months ago by
Joe
21k • written 4.7 years ago by
MB
▴ 50
0
votes
1
reply
3.3k
views
Cutadapt 1.9.1 error
cutadapt
next-gen
updated 10 months ago by
Ram
43k • written 8.2 years ago by
vishweshwaransridhar
▴ 10
20
votes
17
replies
3.2k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by
1769mkc
★ 1.2k • written 3.2 years ago by
pomodoro_sinensis
▴ 110
3
votes
7
replies
3.2k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter
vcftools
sequencing
updated 10 months ago by
Ram
43k • written 4.1 years ago by
IndyDNA
▴ 10
0
votes
1
reply
3.2k
views
How to convert g.vcf to .vcf file
vcf
sequence
genome
alignment
updated 10 months ago by
Ram
43k • written 5.0 years ago by
Sakhaa
• 0
2
votes
10
replies
3.2k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 6 months ago by
Raygozak
★ 1.4k • written 5.8 years ago by
kakukeshi
▴ 80
3
votes
5
replies
3.2k
views
GO annotation for rice in an R package
annotation
R
updated 3 months ago by
prity6459
• 0 • written 7.4 years ago by
djyjin
▴ 10
3
votes
6
replies
3.2k
views
samtools sort not working when using multiple threads
samtools
bam
updated 10 months ago by
Ram
43k • written 2.2 years ago by
bio_elle
▴ 10
6
votes
6
replies
3.2k
views
ChIP-Seq Intensity Analysis
R
ChIP-Seq
updated 11 months ago by
Ram
43k • written 6.4 years ago by
solveforj
▴ 20
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 6 months ago by
Istvan Albert
100k • written 5.9 years ago by
chris.bird
▴ 10
0
votes
1
reply
3.1k
views
PSMC plot (Effective population size)
next-gen
updated 7 months ago by
1601693223
• 0 • written 8.4 years ago by
vicky
▴ 30
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT
TF-footprinting
ATAC-seq
updated 10 months ago by
Ram
43k • written 5.4 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
7
replies
3.1k
views
How much time should be expected for building a database by kraken2-build?
kraken2
updated 11 months ago by
Ram
43k • written 3.2 years ago by
thitrucminh.nguyen
• 0
1
vote
10
replies
3.1k
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 11 months ago by
Ram
43k • written 5.1 years ago by
Kumar
▴ 120
0
votes
3
replies
3.1k
views
From FASTQ to clean BAM using GATK tutorial #6484
gatk
MergeBamAlignment
uBAM
bamclipper
updated 11 months ago by
Ram
43k • written 6.5 years ago by
lamteva.vera
▴ 220
2
votes
6
replies
3.1k
views
hisat2 :Killed (ERR): hisat2-align exited with value 137
RNA-seq
alignment
hisat2
updated 8 months ago by
Ram
43k • written 2.3 years ago by
iamsmor
• 0
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 6 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
3
votes
12
replies
3.0k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 10 months ago by
Pegasus
▴ 100 • written 4.5 years ago by
mnazir
▴ 10
3
votes
6
replies
3.0k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk
variant calling
sureselect
updated 9 months ago by
LeandroF.
• 0 • written 4.2 years ago by
curious
▴ 750
1
vote
5
replies
3.0k
views
Problem in running NOISeq-sim
NOISeq
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.7 years ago by
jaspreetk.dhanjal
▴ 20
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 6 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
2
replies
3.0k
views
How to convert gbk file to roary tool acceptable gff3 format?
linux
bash
python
perl
updated 10 months ago by
Ram
43k • written 3.6 years ago by
Kumar
▴ 120
0
votes
1
reply
2.9k
views
RNA-seq compare FPKM's or fold change of different organisms
gene-expression
FPKM
RNA-seq
fold-change
updated 7 months ago by
Ram
43k • written 6.7 years ago by
jehu
▴ 30
1
vote
4
replies
2.9k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl
ortho
ubuntu
mysql
updated 11 months ago by
Ram
43k • written 5.9 years ago by
wocana
▴ 20
6
votes
9
replies
2.9k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool
Cellranger
NCBI
updated 10 months ago by
Ram
43k • written 2.3 years ago by
aimanbarki
▴ 20
1,000 results • Page
2 of 20
Recent Votes
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
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Recent Replies
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
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: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
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