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388 results • Page
1 of 8
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Views
Votes
Replies
0
votes
0
replies
16
views
How to get a list of genes information for a pathway?
pathway
1 hour ago by
WUSCHEL
▴ 720
0
votes
0
replies
65
views
using GRanges metadata to constrain overlap searches between objects
plyranges
Bioconductor
GRanges
R
GenomicRanges
10 hours ago by
Charles Murtaugh
▴ 40
0
votes
0
replies
65
views
TrN (df = k+5) and TrNe (df = k+2) - which of these Tamura-Nei model variants is used in MEGAx?
Tamura-Nei
phylogeny
phangorn
modelTest
mega
10 hours ago by
poecile.pal
▴ 50
0
votes
0
replies
101
views
How to sort graph based on fold change and instead of activated and suppressed, how to add up and downregulated in graph header?
clusterprofiler
13 hours ago by
sharmatina189059
▴ 110
1
vote
4
replies
191
views
Protein name in GenBank
genbank
python
biopython
updated 9 hours ago by
GenoMax
127k • written 15 hours ago by
Daniel
• 0
0
votes
1
reply
140
views
doing PBS(population branch statistics) in ANGSD
fst
pbs
ANGSD
15 hours ago by
Blessing
• 0
0
votes
0
replies
113
views
How to analyze RepeatProteinMask results
RepeatProteinMask
22 hours ago by
zijian
• 0
0
votes
1
reply
131
views
Tell me about making a transcriptome model of a specific tissue.
model
transcriptome
updated 20 hours ago by
ATpoint
70k • written 22 hours ago by
Soliloquy
▴ 10
0
votes
0
replies
136
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
calling
freebayes
variant
RNA-Seq
22 hours ago by
wlei091226
• 0
0
votes
0
replies
139
views
module and trait correlation for WGCNA
treatment
WGCNA
relation
microarray
module-treatment
1 day ago by
Shriyansh
• 0
0
votes
1
reply
166
views
how to import hdf5 Hi-C data into R using HiTC package
hdf5
importC
R
HiTC
updated 1 day ago by
rpolicastro
11k • written 1 day ago by
rheab1230
▴ 140
0
votes
0
replies
134
views
Emapplot Pie Graphic Legend Interferes with Map
enrichplot
clusterprofiler
Emapplot
1 day ago by
raquel.ajalik
• 0
1
vote
0
replies
138
views
Minimap2 giving opposite strand orientation than Pychopper
nanopore
Pychopper
Minimap2
1 day ago by
vanda.gaonach-lovejoy
▴ 10
0
votes
2
replies
239
views
RNA Sequencing and Vg pan -transcriptome build
fasta
pan-transcriptome
pan-genome
vg
updated 15 hours ago by
Ram
38k • written 1 day ago by
kcarery
• 0
0
votes
0
replies
140
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta
analysis
GWAS
METAL
updated 1 day ago by
GenoMax
127k • written 1 day ago by
ymberzal
• 0
0
votes
4
replies
368
views
Problem with fatsq-dump
fastq-dump
sratoolkit
15 hours ago by
Utpal
• 0
0
votes
0
replies
142
views
ERROR using CIBERSORTx Docker version
deconvolution
version
Docker
CIBERSORTx
22 hours ago by
Leite
★ 1.2k
0
votes
1
reply
214
views
Remove part of headers in FASTA file
Fasta
updated 1 day ago by
GenoMax
127k • written 2 days ago by
fatemeh
• 0
0
votes
2
replies
237
views
Ortholog assembly and extraction
geneious
Ortholog
blast
updated 2 days ago by
dthorbur
▴ 420 • written 2 days ago by
bagdiev39
• 0
0
votes
2
replies
211
views
lncTar
LncRNA
lncTar
maize
updated 2 days ago by
Ram
38k • written 2 days ago by
Amrendra
• 0
1
vote
3
replies
995
views
LncTar error
LncRNA
LncTar
mRNA
updated 2 days ago by
Ram
38k • written 2.1 years ago by
kuntalasb
▴ 10
0
votes
2
replies
243
views
chloroplast genome gaps
genome
gaps
chloroplast
2 days ago by
ugur
• 0
0
votes
0
replies
137
views
Using Lastz aligner
aligner
genome
Lastz
updated 2 days ago by
GenoMax
127k • written 2 days ago by
Diego
▴ 90
1
vote
0
replies
129
views
How to calculate Exon-Intron junction perbase coverage?
RNA-Seq
bedtools
2 days ago by
barrypraveen
▴ 110
0
votes
0
replies
138
views
Extract/include transcript list from GAGE analysis result
RNAseq
GAGE
2 days ago by
farzaneafzali
▴ 70
0
votes
0
replies
125
views
Bam-readcount-installation error
bam-readcount
updated 2 days ago by
Pierre Lindenbaum
153k • written 2 days ago by
shreshta2396
• 0
0
votes
0
replies
120
views
issue changing k values on SOAPdenovo2
novo
de
assembly
2 days ago by
parrasevilla.bioinfo
• 0
0
votes
1
reply
207
views
normalized score for SpatialFeaturePlot
Spatial
Transcriptome
normalization
integration
Seurat
updated 2 days ago by
jv
★ 1.0k • written 2 days ago by
Omics data mining
▴ 210
1
vote
3
replies
331
views
SKAT in R
pvalue
skat
snp
15 hours ago by
Eliza
▴ 20
1
vote
2
replies
260
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 2 days ago by
i.sudbery
16k • written 3 days ago by
rls_08
▴ 40
0
votes
0
replies
173
views
how to look at interaction between SNP and gene
interacting
Hi-C
loop
SNP
Gene
3 days ago by
rheab1230
▴ 140
0
votes
2
replies
208
views
No Passing Variants GATK
calling
variantcalling
GATK
variant
3 days ago by
brandnewatthis
• 0
0
votes
0
replies
208
views
How to calculate the correlation between the expression levels of two genes (features) with Seurat package in scRNA-seq data?
scRNA-seq
Seurat
2 days ago by
sunyeping
▴ 60
0
votes
1
reply
176
views
Gaia CNV error TCGA data
CNV
GAIA
TCGA
updated 3 days ago by
Ram
38k • written 3 days ago by
s.lueong
• 0
0
votes
0
replies
131
views
BULK mRNA-seq with UMIs. Does it make sense to run bedtools genomecov?
RNAseq
gene-length
normalization
3 days ago by
txema.heredia
▴ 70
0
votes
0
replies
115
views
Browsing MGnify IDs and clusters
metagenomics
mgnify
ebi
3 days ago by
biomarco
▴ 20
0
votes
0
replies
118
views
Deeptools clustering differs when clustering sample as standalone and together with other samples
deepTools
3 days ago by
jordi.planells
▴ 450
2
votes
6
replies
312
views
bioinformatics problems solved by graphs data structure
Graph
algorithm
data-structure
updated 3 days ago by
Ram
38k • written 3 days ago by
abdelmalek.benmeziane
• 0
0
votes
1
reply
137
views
Embedded stop codon in translated nucleotide sequences in DAMBE
DAMBE
stop-codon
updated 3 days ago by
Mensur Dlakic
★ 23k • written 3 days ago by
Fathima
• 0
0
votes
1
reply
148
views
ImportError: Bio.Alphabet has been removed from Biopython
Biopython
updated 3 days ago by
Wayne
★ 1.7k • written 3 days ago by
Neel
▴ 10
0
votes
0
replies
109
views
Can't initialise orthomcl schema at orthomclInstallschema step.
mysql
perl
orthomcl
3 days ago by
shivankparashar
• 0
3
votes
2
replies
210
views
correlations in R
cor
R
4 days ago by
rene.j.erhardt
▴ 20
1
vote
2
replies
215
views
Weird looking dispersion & MA plot?
deseq2
RNA-seq
updated 3 days ago by
Ram
38k • written 4 days ago by
Neha
• 0
2
votes
4
replies
240
views
Error with a function in ATAC-seq analysis
ATAC-seq
3 days ago by
Chris
▴ 70
0
votes
0
replies
117
views
how to get genomic range for hi-c datasets in hdf5 file
R
hi-c
contact-map
genomic-ranges
updated 3 days ago by
Ram
38k • written 4 days ago by
rheab1230
▴ 140
0
votes
0
replies
127
views
Samtools: remove unmapped reads as well as reads that are mapped incorrectly
samtools
updated 4 days ago by
Ram
38k • written 4 days ago by
npavliukovec
• 0
0
votes
0
replies
103
views
how to interpret hi-c heatmap hdf5 file
heatmap
maps
hdf5
hi-c
4 days ago by
rheab1230
▴ 140
2
votes
12
replies
523
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 2 days ago by
Ram
38k • written 4 days ago by
Human
• 0
0
votes
0
replies
103
views
Gain of function amplifications - CCLE/cBioPortal
copy
gains
amplification
number
cBioPortal
CCLE
4 days ago by
Lakshmi
▴ 10
0
votes
0
replies
100
views
Biomark Fluidigm delta delta CT method calculation
Fluidigm
Biomark
qPCR
4 days ago by
jms2520
▴ 20
388 results • Page
1 of 8
Recent Votes
A: circos plot gene expression by RNA-Seq
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Popular Question
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Lluís R.
★ 1.2k
Popular Question
to
sharmatina189059
▴ 110
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ahnje770
▴ 20
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Recent Replies
Answer: getTable ignores query ranges
by
Kyle
• 0
The short answer is you can theoretically do this you just need to a) make your SNPs are two base-pairs in length (i.e. add 1 to the end) a…
Answer: Installing rlang version 1.1.0
by
Lluís R.
★ 1.2k
Having a package duplicated means they are at a different `.libPaths()` sites. Check which version is in which directory and directly remov…
Answer: Somatic truth set
by
samuel
▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39
by
Kyle
• 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39
by
Kyle
• 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2
by
vishal.koparde
▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq?
by
lunarskye222
• 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq
by
GenoMax
127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq
by
samuel
▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts?
by
dsull
★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank
by
GenoMax
127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq
by
GenoMax
127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq
by
ATpoint
70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank
by
Mensur Dlakic
★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold
by
ATpoint
70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
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