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122,202 results • Page
676 of 2445
Sort: Rank
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Votes
Replies
0
votes
0
replies
1.1k
views
Correct steps to perform a majority consensus phylogeny in RaxML
phylogeny
raxml
maximum-likelihood
bootstrap
4.6 years ago by
ddh8602
• 0
24
votes
14
replies
7.4k
views
6 follow
How To Generate Dna K-Mers Of A Given Length In C?
c
programming
updated 4.6 years ago by
Ram
45k • written 13.7 years ago by
User 4000
▴ 50
0
votes
0
replies
674
views
should I scale a MASH matrix ?
scale
MASH
4.6 years ago by
v.berriosfarias
▴ 140
2
votes
1
reply
1.2k
views
Independent Filter returns null value with attr(DESeq2Res, 'filterThreshold')
DESeq2
Filtering
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
Kevin
▴ 70
0
votes
3
replies
1.5k
views
Transcript enrichment in Illumina RNAseq
enrichment
transcriptomics
illumina
rnaseq
4.6 years ago by
compuTE
▴ 140
0
votes
2
replies
978
views
Help with MrBayes parameters
Mrbayes
updated 4.6 years ago by
Mensur Dlakic
★ 30k • written 4.6 years ago by
Matthew Aaron
• 0
28
votes
2
replies
7.8k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 3.2 years ago by
eggrandio
▴ 40 • written 4.6 years ago by
Juke34
9.3k
4
votes
4
replies
4.9k
views
Understanding the ColData Matrix
RNA-SEQ
R
Micheal_Love
DESEQ2
updated 4.6 years ago by
Friederike
9.0k • written 4.6 years ago by
raisamathenge
▴ 30
13
votes
14
replies
10.0k
views
9 follow
Tool:
open-cravat: variant annotation tool
open-cravat
updated 2.5 years ago by
Ram
45k • written 7.0 years ago by
slcrick
▴ 260
2
votes
7
replies
6.6k
views
Samtools view error:
bowtie
Samtools
updated 2.7 years ago by
Ram
45k • written 5.1 years ago by
jaqx008
▴ 110
1
vote
1
reply
3.6k
views
sam_hrecs_error Malformed key:value pair
alignment
updated 4.6 years ago by
GenoMax
154k • written 5.8 years ago by
Ric
▴ 440
1
vote
1
reply
1.7k
views
Reactome website gene expression analysis
gene_expression_analysis_tool
Reactome_website
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
camillab.
▴ 160
0
votes
2
replies
1.4k
views
NanoString output: miRNA probe ID with with plus sign (+)
nanostring
mirna
4.6 years ago by
kinnaryshahh
• 0
6
votes
10
replies
3.9k
views
Pacbio SRA data format error
Pacbio
SRA
bax2bam
isoseq3
updated 4.6 years ago by
papodek
▴ 40 • written 4.8 years ago by
shounak.chakraborty1990
▴ 20
0
votes
0
replies
1.1k
views
Error while using pybiomart package
biomart
pybiomart
4.6 years ago by
ahmedmelmoselhy
▴ 20
0
votes
0
replies
828
views
Map LINCS perturbagen identifiers to ChEMBL identifiers?
LINCS
L1000
ChEMBL
4.6 years ago by
n.y.bell
• 0
0
votes
0
replies
1.1k
views
Bowtie2 error: skipping reads
kneaddata
bowtie02
4.6 years ago by
pdhrati02
▴ 30
7
votes
4
replies
2.1k
views
very short 'time series' bulk rna-seq, testing two conditions
rna
data
updated 4.6 years ago by
ATpoint
90k • written 4.7 years ago by
joha
▴ 10
6
votes
8
replies
2.2k
views
Joining blast hits together into single fasta sequence
sequence
genomics
blast
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
Wilber0x
▴ 70
0
votes
0
replies
915
views
D Prime GWAS
Linkage
GWAS
4.6 years ago by
Filago
▴ 110
0
votes
0
replies
714
views
Metabolite identification from m/z and retention time
metabolomics
R
4.6 years ago by
mm2568
• 0
0
votes
0
replies
1.0k
views
TPM biological replicates, geometric mean
TPM
tsi
tissue
4.6 years ago by
joha
▴ 10
19
votes
9
replies
3.5k
views
8 follow
Forum:
Future of Microarrays
Microarrays
updated 4.6 years ago by
Joe
22k • written 4.6 years ago by
E
▴ 20
3
votes
2
replies
1.3k
views
Key and value parse with regex
python
regex
updated 4.6 years ago by
JC
13k • written 4.6 years ago by
enes
▴ 40
0
votes
2
replies
1.4k
views
How to use DownsampleSam quickly and efficiently with multiple PROBABILITies?
picard
downsampling
RNA-seq
BAM
4.6 years ago by
-IvanWoo-
• 0
0
votes
0
replies
1.1k
views
differential gene expression (DGE) using TCGABiolinks
DGE
TCGA
tcgabiolinks
4.6 years ago by
peter
▴ 20
2
votes
6
replies
2.6k
views
RRBS ANNOTATION
NGS
ANNOTATION
RRBS
4.6 years ago by
GiV17
▴ 50
0
votes
4
replies
1.7k
views
Gatk bam metrics
ngs
metrics
Gatk
bam
updated 3.7 years ago by
Ram
45k • written 4.6 years ago by
Sabeen
▴ 30
1
vote
1
reply
1.7k
views
split vcf file into multiple files
WGS
vcf
bcftools
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
lz1903
▴ 10
3
votes
8
replies
2.8k
views
Convertion Of Gff3 To Gtf
gtf
gff
4.6 years ago by
daalsa98
▴ 10
59
votes
23
replies
55k
views
14 follow
Bam File: Change Chromosome Notation
samtools
bam
updated 4.5 years ago by
zx8754
12k • written 14.1 years ago by
Lisanne
▴ 160
3
votes
3
replies
1.3k
views
Phylogenetic tree of gene clusters
evolution
clusters
phylogeny
updated 4.6 years ago by
Joe
22k • written 4.6 years ago by
A_heath
▴ 180
2
votes
2
replies
9.7k
views
[E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam'
rna-seq
4.6 years ago by
jenyfer
▴ 10
0
votes
2
replies
1.6k
views
NIPT related tools & software
NIPS
4.5 years ago by
smrutimayipanda
▴ 20
15
votes
4
replies
8.2k
views
TMM-Normalization
TMM
RNAseq-Normalization
updated 7 weeks ago by
kalavattam
▴ 380 • written 4.6 years ago by
Filago
▴ 110
0
votes
0
replies
841
views
How to annotate variants against hs37d5?
SNP
annotation
4.6 years ago by
vinayjrao
▴ 260
1
vote
2
replies
1.3k
views
genomicdbImport issue
genomicdbImport
gatk
4.5 years ago by
ijlal.hyder2012
▴ 20
0
votes
3
replies
1.7k
views
Skewed Betweenness Centrality values resulting in almost unusable PPI networks for my university project - what can I do?
Cytoscape
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
gemmalouisebaldock
▴ 20
0
votes
0
replies
826
views
How to sort and rank compounds docked with AutoDock Vina when the result is presented as only single decimal number?
Docking
autodockVina
VS
VirtualScreening
4.6 years ago by
srdjanmasirevic2
▴ 20
0
votes
1
reply
2.0k
views
RagTag assembly after spades
spades
conting
ragtag
scaffolds
updated 4.6 years ago by
samuel.a.odonnell
▴ 640 • written 4.6 years ago by
anithanagaraj93
▴ 10
9
votes
4
replies
15k
views
Installing perl modules on a conda environment produce changes out of the environment?
conda
perl
updated 4.6 years ago by
Philipp Bayer
8.9k • written 4.6 years ago by
v.berriosfarias
▴ 140
1
vote
0
replies
1.0k
views
Codon alignment with degenerate nucleotides?
paml
codeml
codon
alignment
4.6 years ago by
DNAlias
▴ 40
3
votes
1
reply
5.7k
views
add patient information to the metadata or Make New Orig.ident in seurat object
R
RNA-SEQ
Seurat
4.6 years ago by
Maria17
▴ 40
2
votes
3
replies
1.7k
views
RNAseq
stringtie
rnaseq
error
gffcompare
4.6 years ago by
mtavakoli4030
▴ 10
1
vote
2
replies
2.9k
views
Duplicated Gene Symbol names after geneID conversion
geneID
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
asumani
▴ 70
1
vote
1
reply
1.4k
views
How to merge two GTFs which share some common features
stringtie
GTF
annotation
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
emalekos
▴ 40
0
votes
0
replies
1.1k
views
my gffcompare out put gtf file is like that. on complete row is followed by some uncomplete row wich have not class codes.
gffcompare
rna
lncrna
gtf
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
mtavakoli4030
▴ 10
1
vote
1
reply
1.2k
views
Performance metrics of aligners and variant callers
benchmarking
WGS
updated 4.6 years ago by
Jeremy Leipzig
23k • written 4.6 years ago by
Prashant
▴ 10
2
votes
2
replies
1.7k
views
News:
Bioinformatics Solutions on AWS
Cloud
AWS
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
Jillian
▴ 20
9
votes
13
replies
3.6k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq
DESeq2
updated 4.6 years ago by
Ram
45k • written 4.6 years ago by
sumitguptabt
▴ 30
122,202 results • Page
676 of 2445
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Comment: Visualize methylation status in Pacbio Hifi read
by
cmdcolin
★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets
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154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
samuel.a.odonnell
▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
Pierre Lindenbaum
166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
xinguok794
▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics
by
Kent
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Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around
by
Luca Arbore
▴ 10
Thank you very much Kevin, it worked!
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