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121,919 results • Page
708 of 2439
Sort: Rank
Rank
Views
Votes
Replies
4
votes
10
replies
3.7k
views
How to count the number of codons in a frame or order using the equation?
biopython
python
code
4.6 years ago by
USER
• 0
0
votes
0
replies
773
views
How to align multiple fastq files with Hisat2 ?
rna-seq
4.6 years ago by
sarai
• 0
2
votes
6
replies
3.9k
views
is there any solution to convert a multifasta file to csv?
fasta
biopython
perl
updated 2.2 years ago by
Ram
45k • written 4.7 years ago by
USER
• 0
0
votes
5
replies
1.3k
views
Insert data with pymysql into a database mysql error. How to solve?
python
database
biopython
mysql
genome
4.6 years ago by
USER
• 0
0
votes
1
reply
743
views
rna-seq/DEseq2 analysis - is it a linear combination problem?
RNA-Seq
deseq2
updated 4.6 years ago by
ATpoint
89k • written 4.6 years ago by
aabbcc1
• 0
1
vote
1
reply
874
views
Loading a dataset via acession number
R
sequencing
updated 4.6 years ago by
ATpoint
89k • written 4.6 years ago by
angus.j.g.campbell
▴ 10
0
votes
2
replies
1.3k
views
Variant calling tool for Bacterial NGS data
SNP
Variant calling
Bacterial
GATK
updated 4.6 years ago by
Biostar
20 • written 4.6 years ago by
Boberoni
▴ 20
0
votes
0
replies
613
views
What could be a good strategy to describe GO enrichments for a pubblication?
GO
4.6 years ago by
Firingam
▴ 30
1
vote
1
reply
11k
views
How to change Rstudio language
R
updated 4.6 years ago by
ATpoint
89k • written 4.6 years ago by
Fede_Santos95
▴ 20
0
votes
3
replies
1.4k
views
Chip-seq IgG as control or Input DNA or usage of both
ChIP-Seq
next-gen
sequencing
4.6 years ago by
luckysardar171
▴ 20
0
votes
1
reply
1.5k
views
How to average normalized counts of biological replicates
RNA-Seq
R
4.6 years ago by
marina.rot
• 0
2
votes
9
replies
2.1k
views
Which normalization method/pipeline is best to generate normalized counts to make different single cell experiments comparable
single cell
normalization
updated 4.6 years ago by
Mensur Dlakic
★ 30k • written 4.6 years ago by
amjass
▴ 20
3
votes
1
reply
1.6k
views
determine the robustness of single-cell clusters
clustering
RNA-Seq
rna-seq
R
Seurat
updated 4.6 years ago by
fracarb8
★ 1.7k • written 4.6 years ago by
Maria17
▴ 40
4
votes
6
replies
3.4k
views
cannot download refseq genomes
refseq
updated 2.5 years ago by
Ram
45k • written 4.6 years ago by
sapuizait
▴ 10
5
votes
4
replies
1.4k
views
Extract column which contain <20 exons in a transcript
transcript
exons
extract
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
harry
▴ 40
2
votes
2
replies
1.9k
views
MultiBigwigSummary of deepTools keeps on running for a long time
ChIP-Seq
multibigwigsummary
deeptools
ubuntu
updated 3.8 years ago by
Friederike
9.0k • written 4.6 years ago by
saha.shagnik
• 0
0
votes
5
replies
1.9k
views
command line Ncbi Blast SRA remote
ncbi
blast
sra
updated 4.6 years ago by
GenoMax
153k • written 4.6 years ago by
acx01c
• 0
0
votes
0
replies
713
views
Finding the logic of lncRNA effect on gene expression
lncRNA
Gene expression
RNA
updated 4.6 years ago by
Biostar
20 • written 4.6 years ago by
MRezaei
▴ 40
0
votes
0
replies
674
views
What is after WGCNA for co-expressed genes?
R
wgcna
protein-protein-interaction
4.6 years ago by
Omar Mohamed
• 0
0
votes
1
reply
760
views
something about mirDeep2 error
software error
updated 4.6 years ago by
ATpoint
89k • written 4.6 years ago by
972050141
• 0
0
votes
0
replies
435
views
An error occurred while running CRISP for calling variant
software error
4.6 years ago by
445014525
• 0
0
votes
0
replies
820
views
A list of plant (Arabidopsis, rice or maize) cell cycle genes for Seurat
single cell
seurat
cell cycle
scRNA-seq
4.6 years ago by
slbai00001
• 0
2
votes
8
replies
2.9k
views
Ignore replacing a comma within quotes
sed
awk
regex
4.6 years ago by
vinayjrao
▴ 260
4
votes
7
replies
1.7k
views
Fasta and csv file reformatting
sed
awk
fasta
csv
updated 4.6 years ago by
Biostar
20 • written 4.6 years ago by
MSRS
▴ 590
4
votes
6
replies
9.1k
views
How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?
gene
RNA-Seq
updated 3.3 years ago by
mfro
• 0 • written 5.4 years ago by
jzhongqiang
• 0
0
votes
4
replies
1.3k
views
How do I know bcftools mpileup command completed?
bcftools
mpileup
DNA-seq
4.6 years ago by
gt
▴ 30
1
vote
0
replies
3.5k
views
Functional annotation(GO,KEGG): Blast2GO+KAAS or EggNOG
blast2go
eggnog
kegg
rna-seq
genome
updated 4.6 years ago by
Biostar
20 • written 5.4 years ago by
tianshenbio
▴ 190
0
votes
8
replies
1.7k
views
Bacterial RNA-SEQ - Quality Control
RNA-Seq
updated 4.6 years ago by
swbarnes2
15k • written 4.6 years ago by
Sammy
▴ 30
0
votes
5
replies
2.3k
views
umi_tools using regex greedy quantifiers only returning 1 character
regex
umi_tools
updated 2.3 years ago by
Ram
45k • written 4.6 years ago by
williamtmills
▴ 20
0
votes
4
replies
2.2k
views
Where can I find data about gene expression in such diseases as bipolar (maniacal/depressive phases), depression, paranoia?
gene
expression
desease
database
updated 4.6 years ago by
seidel
11k • written 4.6 years ago by
philosophical.raptor111
• 0
2
votes
13
replies
2.3k
views
complexheatMap runtime error
Complexheatmap
R
updated 4.6 years ago by
Biostar
20 • written 4.7 years ago by
amitpande74
▴ 20
6
votes
11
replies
1.8k
views
Recommendations for genome-wide genotyping platform, array and data analysis software?
genotyping
4.6 years ago by
anamaria
▴ 220
7
votes
7
replies
6.4k
views
RNA-seq ribosomal genes vs proteins
RNA-Seq
scRNA-seq
rRNA
updated 4.6 years ago by
predeus
★ 2.1k • written 4.6 years ago by
igor
13k
6
votes
5
replies
2.1k
views
Kept getting issue when using ImmGenData() in SingleR
R
SingleR
4.6 years ago by
leranwangcs
▴ 150
2
votes
3
replies
1.3k
views
Combine two independent Seurat analysis into a single one
RNA-Seq
seurat
updated 4.6 years ago by
Ram
45k • written 4.6 years ago by
elb
▴ 260
2
votes
1
reply
3.1k
views
Interpreting ATAC-SEQ motif enrichment output
ATAC-Seq
ChIP-Seq
updated 4.6 years ago by
ATpoint
89k • written 4.6 years ago by
emalekos
▴ 40
5
votes
5
replies
2.7k
views
How to select a "representative" transcript in multiple transcript variants from annotation with ANNOVAR and gencode
annovar
gencode
transcript
SNP
annotation
4.6 years ago by
svlachavas
▴ 790
1
vote
3
replies
1.3k
views
Retrieve unique human membrane protein coding genes in Uniprot
Uniprot
membrane proteins
human genome
updated 4.6 years ago by
Elisabeth Gasteiger
★ 2.4k • written 4.6 years ago by
PRog
▴ 10
1
vote
6
replies
2.6k
views
Problems removing specific contig from .bam file
samtools
WGS
bam
genome
picard
updated 2.5 years ago by
Ram
45k • written 4.6 years ago by
USA_225478
• 0
0
votes
3
replies
1.2k
views
Bacterial (E.coli) RNA-SEQ differential gene expression (with pET system)
rna-seq
updated 4.6 years ago by
Joe
22k • written 4.6 years ago by
Sammy
▴ 30
5
votes
1
reply
1.6k
views
News:
Paid opportunity: need microbiome experts for a survey and test of robustness
survey
updated 2.6 years ago by
Ram
45k • written 5.0 years ago by
Jeremy Leipzig
23k
0
votes
1
reply
1.3k
views
News:
The NCBI Datasets command-line tool now provides ortholog data
ncbi
gene
json
refseq
updated 2.6 years ago by
Ram
45k • written 4.6 years ago by
e.cox
▴ 50
13
votes
3
replies
7.0k
views
Forum:
Can We Have A Collection Of Interesting Research Topics?
project
phd
updated 2.6 years ago by
Ram
45k • written 13.3 years ago by
Michael
56k
3
votes
1
reply
4.7k
views
Three way comparison RNAseq libraries
RNA-Seq
R
Analysis
updated 2.7 years ago by
Ram
45k • written 10.3 years ago by
rodrigo.nicodemos82
▴ 10
0
votes
6
replies
2.3k
views
What are the best quantification tools for miRNA seq?
miRNA
RNA-Seq
Salmon
miRNA-seq
4.6 years ago by
cecilomar6
• 0
3
votes
2
replies
911
views
What dataset do I use to annotate a transcriptome? Another transcriptome or a genome?
alignment
RNA-Seq
updated 3.7 years ago by
lieven.sterck
15k • written 4.6 years ago by
pseudacris
▴ 10
1
vote
4
replies
1.2k
views
How to convert the position of probes into Gene symbol or Entrez_id(Platform GPL16110)
geo
updated 2.2 years ago by
Ram
45k • written 4.6 years ago by
linhzye
▴ 10
0
votes
1
reply
1.0k
views
Breast cancer expression data with subtype information
breast cancer
data
subtype
expression
dataset
4.6 years ago by
sabin
▴ 50
0
votes
0
replies
596
views
How can I convert the transcript coordinate to a genomic coordinate?
RNA-Seq
Assembly
sequence
4.6 years ago by
qwesxadzc9
• 0
0
votes
5
replies
1.9k
views
Mapping a short primer sequence to a whole genome
alignment
updated 4.6 years ago by
shenwei356
8.7k • written 4.6 years ago by
robert.murphy
▴ 110
121,919 results • Page
708 of 2439
Recent Votes
A: Binning Over Genes And Calculating The Coverage [Bedops/Bedmap]
Answer: [vg giraffe] Unable to add read group to BAM file
Comment: [vg giraffe] Unable to add read group to BAM file
Answer: [vg giraffe] Unable to add read group to BAM file
Answer: vcf multisample
Answer: vcf multisample
Answer: vcf multisample
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Recent Replies
Comment: Help with species tree with orthofinder, iqtree and branch labeling
by
GenoMax
153k
> I don’t have clear species labels in my headers, only sequence IDs. I have not used iqtree, so this is only a thought ... should it be y…
Comment: Help with species tree with orthofinder, iqtree and branch labeling
by
san96
▴ 190
Thank you so much.
Comment: [vg giraffe] Unable to add read group to BAM file
by
saruman
▴ 10
Yes, it seems so. Thank you.
Comment: cellranger mkref fail/error
by
GenoMax
153k
> The thing is that I do not have a genome for these organisms. That is not what `cellranger mkref` is expecting. You could consider alt…
Comment: cellranger mkref fail/error
by
tatsispolychronis
• 0
The thing is that I do not have a genome for these organisms. i made a transcriptome using TRinity and this is what I am feeding it. I do n…
Comment: Genome Assembly QC from BAM files
by
SomeOne
▴ 240
Hi, I am not sure if i can call them good assemblies. Although based on QUAST and BUSCO stats, everything looks too good but somehow i hav…
Comment: cellranger mkref fail/error
by
GenoMax
153k
You need to provide the genome reference for the `--fasta` option as noted in https://www.10xgenomics.com/support/software/cell-ranger/late…
Answer: Methods to analyse structural similarity: co-evolution vs convergence
by
Joe
22k
Without historical data (ancient DNA) there's no way to ever really know this for certain. The best we can do is make inferences based on t…
Answer: vcf multisample
by
Pierre Lindenbaum
166k
eg : https://ega-archive.org/datasets/EGAD50000001683 > Merged VCF file from sporadic Meniere disease cohort (found using https://dat…
Comment: Genome Assembly QC from BAM files
by
GenoMax
153k
Since this saga has been on going for a long time, it will be helpful to add a comment as to how you finally got to this point of what seem…
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by
dthorbur
★ 3.1k
A few comments. 1. Coevolution of a trait between 2 organisms can end up with a convergent structure with another organism. It's not e…
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by
SomeOne
▴ 240
Thank you. Based on the description these two look really what i wanted to see.
Comment: miRNA low mapping ratings
by
i.sudbery
22k
Also, can you just clarify that the output above is from cutadapt or form miRDeep2?
Comment: miRNA low mapping ratings
by
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22k
What happens if you remove the `--minimum-length` requirement to cutadapt, and then run fastqc on the result - what size disitribution do y…
Answer: Genome Assembly QC from BAM files
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7.9k
You can have a look at the tools in the PAQman pipeline https://github.com/SAMtoBAM/PAQman, and maybe also Inspector https://github.com/Mag…
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