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385 results • Page
1 of 8
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Rank
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Votes
Replies
0
votes
1
reply
41
views
Ortholog assembly and extraction
geneious
Ortholog
blast
updated 2 hours ago by
GenoMax
127k • written 3 hours ago by
bagdiev39
• 0
0
votes
2
replies
77
views
lncTar
LncRNA
lncTar
maize
updated 5 hours ago by
Ram
38k • written 6 hours ago by
Amrendra
• 0
1
vote
3
replies
871
views
LncTar error
LncRNA
LncTar
mRNA
updated 5 hours ago by
Ram
38k • written 2.1 years ago by
kuntalasb
▴ 10
0
votes
2
replies
73
views
chloroplast genome gaps
genome
gaps
chloroplast
52 minutes ago by
ugur
• 0
0
votes
0
replies
47
views
Using Lastz aligner
aligner
genome
Lastz
updated 6 hours ago by
GenoMax
127k • written 6 hours ago by
Diego
▴ 90
0
votes
0
replies
64
views
Understanding multifactor designs and control variables in DESeq2
RNA-seq
DESeq2
updated 19 minutes ago by
Ram
38k • written 6 hours ago by
kldsajf;ldsj;l
• 0
1
vote
0
replies
46
views
How to calculate Exon-Intron junction perbase coverage?
RNA-Seq
bedtools
6 hours ago by
barrypraveen
▴ 110
0
votes
0
replies
52
views
Extract/include transcript list from GAGE analysis result
RNAseq
GAGE
7 hours ago by
farzaneafzali
▴ 70
0
votes
0
replies
51
views
Bam-readcount-installation error
bam-readcount
updated 7 hours ago by
Pierre Lindenbaum
153k • written 8 hours ago by
shreshta2396
• 0
0
votes
0
replies
44
views
issue changing k values on SOAPdenovo2
novo
de
assembly
8 hours ago by
parrasevilla.bioinfo
• 0
0
votes
1
reply
67
views
Problem with fatsq-dump
fastq-dump
sratoolkit
updated 8 hours ago by
GenoMax
127k • written 8 hours ago by
Utpal
• 0
0
votes
1
reply
114
views
normalized score for SpatialFeaturePlot
Spatial
Transcriptome
normalization
integration
Seurat
updated 5 hours ago by
jv
★ 1.0k • written 12 hours ago by
Omics data mining
▴ 210
1
vote
2
replies
168
views
SKAT in R
pvalue
skat
snp
updated 5 hours ago by
Pierre Lindenbaum
153k • written 14 hours ago by
Eliza
▴ 20
0
votes
0
replies
100
views
WGCNA
conncetivity
wgcna
15 hours ago by
ali
• 0
1
vote
2
replies
184
views
in an RNA-seq experiment, what threshold would you use to define a set of expressed or active genes in a cell line?
RNA-seq
updated 10 hours ago by
i.sudbery
16k • written 21 hours ago by
rls_08
▴ 40
0
votes
0
replies
108
views
how to look at interaction between SNP and gene
interacting
Hi-C
loop
SNP
Gene
21 hours ago by
rheab1230
▴ 140
0
votes
2
replies
151
views
No Passing Variants GATK
calling
variantcalling
GATK
variant
21 hours ago by
brandnewatthis
• 0
0
votes
0
replies
117
views
How to calculate the correlation between the expression levels of two genes (features) with Seurat package in scRNA-seq data?
scRNA-seq
Seurat
5 hours ago by
sunyeping
▴ 50
0
votes
1
reply
131
views
Gaia CNV error TCGA data
CNV
GAIA
TCGA
updated 1 day ago by
Ram
38k • written 1 day ago by
s.lueong
• 0
0
votes
0
replies
105
views
BULK mRNA-seq with UMIs. Does it make sense to run bedtools genomecov?
RNAseq
gene-length
normalization
1 day ago by
txema.heredia
▴ 70
0
votes
0
replies
96
views
Browsing MGnify IDs and clusters
metagenomics
mgnify
ebi
1 day ago by
biomarco
▴ 20
0
votes
0
replies
95
views
Deeptools clustering differs when clustering sample as standalone and together with other samples
deepTools
1 day ago by
jordi.planells
▴ 450
2
votes
6
replies
276
views
bioinformatics problems solved by graphs data structure
Graph
algorithm
data-structure
updated 1 day ago by
Ram
38k • written 1 day ago by
abdelmalek.benmeziane
• 0
0
votes
1
reply
118
views
Embedded stop codon in translated nucleotide sequences in DAMBE
DAMBE
stop-codon
updated 1 day ago by
Mensur Dlakic
★ 23k • written 1 day ago by
Fathima
• 0
0
votes
1
reply
138
views
ImportError: Bio.Alphabet has been removed from Biopython
Biopython
updated 1 day ago by
Wayne
★ 1.6k • written 1 day ago by
Neel
▴ 10
0
votes
0
replies
106
views
Can't initialise orthomcl schema at orthomclInstallschema step.
mysql
perl
orthomcl
1 day ago by
shivankparashar
• 0
3
votes
2
replies
199
views
correlations in R
cor
R
1 day ago by
rene.j.erhardt
▴ 20
1
vote
2
replies
209
views
Weird looking dispersion & MA plot?
deseq2
RNA-seq
updated 1 day ago by
Ram
38k • written 1 day ago by
Neha
• 0
2
votes
4
replies
223
views
Error with a function in ATAC-seq analysis
ATAC-seq
1 day ago by
Chris
▴ 70
0
votes
0
replies
113
views
how to get genomic range for hi-c datasets in hdf5 file
R
hi-c
contact-map
genomic-ranges
updated 1 day ago by
Ram
38k • written 1 day ago by
rheab1230
▴ 140
0
votes
0
replies
123
views
Samtools: remove unmapped reads as well as reads that are mapped incorrectly
samtools
updated 1 day ago by
Ram
38k • written 1 day ago by
npavliukovec
• 0
0
votes
0
replies
102
views
how to interpret hi-c heatmap hdf5 file
heatmap
maps
hdf5
hi-c
2 days ago by
rheab1230
▴ 140
2
votes
12
replies
494
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 6 hours ago by
Ram
38k • written 2 days ago by
Human
• 0
0
votes
0
replies
102
views
Gain of function amplifications - CCLE/cBioPortal
copy
gains
amplification
number
cBioPortal
CCLE
2 days ago by
Lakshmi
▴ 10
0
votes
0
replies
97
views
Biomark Fluidigm delta delta CT method calculation
Fluidigm
Biomark
qPCR
2 days ago by
jms2520
▴ 20
0
votes
0
replies
91
views
pyscenic cannot mapped to the feather file
pyscenic
2 days ago by
Andy
▴ 30
0
votes
0
replies
84
views
How to calculate Summary.csv statistics after re-running STARSolo cell filtering?
scRNA-seq
STARSolo
STAR
2 days ago by
ayeTown
• 0
0
votes
0
replies
96
views
Solving set of equations possibly with Matlab for affinity measurement with ELISA
set
ELISA
affinity
Matlab
equation
2 days ago by
field654
▴ 30
0
votes
0
replies
96
views
how to get the nucleotide squence behind a symbolic ALT in VCF
SV
vcf
sniffles
1 hour ago by
Maxine
• 0
0
votes
0
replies
154
views
How can I retrive the actual amino acid and the alternative amino acid (if any cordon changes happened due to editing)?
RNA
editing
2 days ago by
Genetics
▴ 20
0
votes
0
replies
87
views
pyscenic feather file
pyscenic
2 days ago by
Andy
▴ 30
1
vote
1
reply
145
views
Is there a site that takes a list of uniprot IDs/gene IDs as input and create radial phylogenetic tree?
phylogenetictree
2 days ago by
Diwan
▴ 650
0
votes
0
replies
85
views
Something wrong with my code concerning bsseq visualization
bsseq
plotRegion
R
2 days ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
93
views
How to bifurcate patients into high and low expressing groups for TCGA survival analysis for a gene of interest
Meidan
TCGA
Percentile
Survival
R
2 days ago by
Manav
• 0
1
vote
3
replies
187
views
TSV with multi-allelic sites to VCF
bcftools
updated 1 day ago by
barslmn
★ 1.3k • written 2 days ago by
Christian
▴ 20
0
votes
0
replies
107
views
Spearman correlation rna-seq gene to blood values
spearman
rna-seq
1 day ago by
bas2020
▴ 20
0
votes
0
replies
71
views
Outgroup for plastome NJ-tree (from pseudoalignment based on SNPs)
bwa-mem2
samtools
freebayes
mega
vcf2phylip
2 days ago by
poecile.pal
▴ 50
4
votes
3
replies
179
views
Geom bar postive and negative values in a flipped plot
flip_coord
ggplot
geom_bar
1 day ago by
luzglongoria
▴ 40
3
votes
8
replies
279
views
getting coding exon information from Ensembl API
Ensembl
API
updated 2 days ago by
Ram
38k • written 2 days ago by
Nobody
▴ 30
0
votes
0
replies
100
views
displaying results of different RNA-seq projects in R shiny
RNA-seq
shiny
R
2 days ago by
rls_08
▴ 40
385 results • Page
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Answer: Using STAR for RNA seq-alignment.
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blastn command line returning empty file
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Answer: How to demultiplex single end - dual index run - NextSeq 500
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GenoMax
127k
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randalljellis
▴ 90
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RvV
▴ 10
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farzaneafzali
▴ 70
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Recent Replies
Comment: chloroplast genome gaps
by
ugur
• 0
after alignment, it occurs in different sizes of gaps
Answer: Cellranger sequencing
by
ATpoint
70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
Answer: Assembly at lineage level from shotgun data ?
by
Mensur Dlakic
★ 23k
The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a referenc…
Comment: Ortholog assembly and extraction
by
GenoMax
127k
Many seem to use `orthofinder` for this purpose. See if it is useful: https://github.com/davidemms/OrthoFinder
Answer: Python formatting when visualizing Primer3-py dimers
by
Wayne
★ 1.6k
Try this so you'll see that using [tabulate](https://github.com/astanin/python-tabulate) to print the dataframe causes it to respect the li…
Comment: Python formatting when visualizing Primer3-py dimers
by
bhumm
▴ 30
Glad I am making this more clear. The 'test1' in practice will be the 'primer name' to allow for tracking of other metrics (Tm, hairpin str…
Comment: Python formatting when visualizing Primer3-py dimers
by
Wayne
★ 1.6k
Starting to understand what you want and why. My question is now also then do you actually want the brackets? They seem to shift the rela…
Comment: Python formatting when visualizing Primer3-py dimers
by
bhumm
▴ 30
Hi Wayne, Thanks for the response. I have updated the code to be more representative of the toy example I have provided - apologies for an…
Comment: chloroplast genome gaps
by
Pierre Lindenbaum
153k
> , but the alignment results show different size gaps. what does it mean ?
Comment: lncTar
by
Ram
38k
I see that you added an answer to a 2 year old post. Don't do that - what you added was "I have this problem too" comment, not an answer. I…
Comment: LncTar error
by
Ram
38k
Do not add answers unless you're answering the top level question. Given that you've opened a new question, I'm deleting this post.
Comment: Samtools fixmate: whta's wrong with the terminal?
by
Ram
38k
Lol I started writing first, then discovered each issue as I was writing. All I saw was the `-0` but then oh my goodness, so many problems!
Comment: SKAT in R
by
Pierre Lindenbaum
153k
cross-posted: https://bioinformatics.stackexchange.com/questions/20772
Comment: Samtools fixmate: whta's wrong with the terminal?
by
Pierre Lindenbaum
153k
oh , Ram was too fast ! :-D
Answer: Samtools fixmate: whta's wrong with the terminal?
by
Pierre Lindenbaum
153k
1) your [standard][1] output is redirected to the terminal instead of a [file][2]. 2) there is no such option `-0` (zero) . your want …
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