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785 results • Page
3 of 16
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Views
Votes
Replies
8
votes
5
replies
1.6k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 5 days ago by
Ram
40k • written 24 months ago by
A_heath
▴ 140
0
votes
2
replies
1.5k
views
Question about REDItools
REDItools
updated 10 days ago by
Ethan Lee
• 0 • written 4.1 years ago by
tujuchuanli
▴ 100
2
votes
20
replies
1.5k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
20 days ago by
Maxine
▴ 30
3
votes
4
replies
1.5k
views
Reference implementation rejects step without inputs
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 6.8 years ago by
unduthegun
• 0
2
votes
3
replies
1.5k
views
Can I use output eval with CWL to create the list of output files (i.e. replace the glob results)?
Common-Workflow-Language
CWL
updated 15 days ago by
Ram
40k • written 4.4 years ago by
mavrommatis.konstantinos
▴ 10
0
votes
7
replies
1.5k
views
what does "total read count" means in fastqc file. how does it helpful for analysis
fastqc
updated 7 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
1
vote
9
replies
1.5k
views
Scanpy Pearson residual PCA error
python
scRNA
scanpy
PCA
updated 4 days ago by
Ram
40k • written 13 months ago by
Emily
▴ 30
2
votes
3
replies
1.5k
views
Racon command line with paired-ends Illumina reads
Illumina
Racon
updated 5 days ago by
Ram
40k • written 2.1 years ago by
A_heath
▴ 140
2
votes
13
replies
1.5k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 13 hours ago by
Ram
40k • written 5 weeks ago by
epianalysis
• 0
2
votes
2
replies
1.5k
views
CWL : default value and label for argument
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 7.0 years ago by
sebastien.letort
▴ 70
1
vote
5
replies
1.4k
views
--preserve_environment with docker containers?
cwltool
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 6.0 years ago by
Biowoogles
▴ 20
0
votes
1
reply
1.4k
views
NS, AC, AN and AF in VCF file
VCF
updated 21 days ago by
Mwangana
• 0 • written 14 months ago by
wangdp123
▴ 310
2
votes
7
replies
1.4k
views
How to find newline character in fastq file? Is it essential to remove them?
FASTQ
updated 7 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
6
votes
8
replies
1.4k
views
"Simplifying" a very fragmented genome for visualisation?
reference-genome
visualisation
fasta
updated 21 days ago by
Ram
40k • written 2.0 years ago by
setschmann
▴ 10
2
votes
2
replies
1.4k
views
rerunning workflows with --cachedir sometimes repeats steps despite no changes to input
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 7.0 years ago by
c.ravarani
• 0
2
votes
4
replies
1.3k
views
How to get mm39 repeatmasker track from UCSC genome browser
genome
ucsc
updated 18 days ago by
bioinfo_wen
▴ 10 • written 22 months ago by
saarantras
▴ 20
0
votes
3
replies
1.3k
views
how to calculate BAF and LRR from VCF or BCF files?
SNP
BAF
LRR
Variation
5 days ago by
xiaoguang
▴ 130
1
vote
4
replies
1.3k
views
ConsensusClusterPlus: How to extract most contributing features for each cluster
R
consensusclusterplus
updated 7 days ago by
LChart
3.4k • written 2.6 years ago by
komal.rathi
★ 4.1k
9
votes
6
replies
1.3k
views
6 follow
Forum:
GTF files from Ensembl Releases 105 and 106 unsorted
Ensembl
bug
GTF
updated 13 days ago by
ATpoint
76k • written 10 months ago by
dlaehnemann
▴ 30
8
votes
7
replies
1.2k
views
Whole genome species clustering
phylogeny
assembly
phylogenetics
updated 28 days ago by
pmiller
• 0 • written 2.4 years ago by
robert.murphy
▴ 80
3
votes
1
reply
1.2k
views
%% error in Rstudio
seurat
r
updated 4 days ago by
Ram
40k • written 2.1 years ago by
AbsaR
• 0
1
vote
1
reply
1.2k
views
CWL: Input restrictions for integers
Common-Workflow-Language
CWL
updated 15 days ago by
Ram
40k • written 6.3 years ago by
schujo
▴ 10
9
votes
4
replies
1.2k
views
How to extend contigs from single-end reads?
contigs
contig-extension
updated 5 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
6
votes
7
replies
1.2k
views
wc -l or wc -c which linux command is best to find total read count in fastq file?
linux
updated 7 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
2
votes
1
reply
1.2k
views
same query but different results (TCGAbiolinks vs TCGA Portal)
R
RNA-Seq
25 days ago by
tyasird
▴ 10
10
votes
11
replies
1.2k
views
Seeking feedback on ChIP-seq normalization method: Calculating scaling factors by dividing input by IP, including spike-in
coverage
spike-in
scaling-factor
ChIP-seq
18 days ago by
kalavattam
▴ 180
6
votes
4
replies
1.2k
views
How to sort blast results by a minimum % of identical matches?
blast
updated 5 days ago by
Ram
40k • written 2.9 years ago by
A_heath
▴ 140
2
votes
2
replies
1.2k
views
How to convert genotypes "1, 2" to "0,1, 2"?
snp
plink
updated 20 days ago by
karthivalarmathi99
▴ 10 • written 2.2 years ago by
Emy
▴ 50
1
vote
2
replies
1.1k
views
Why is chromHMM's binarizeBed with the -peaks argument not recommended for broad peaks?
chromHMM
macs2
chipseq
cut&run
cutandrun
updated 22 days ago by
e.r.zakiev
▴ 80 • written 3.0 years ago by
Melinda
• 0
9
votes
4
replies
1.1k
views
Illumina Q score
Illumina
quality-score
updated 5 days ago by
Ram
40k • written 2.0 years ago by
A_heath
▴ 140
8
votes
17
replies
1.1k
views
7 follow
How to limit fasta header to 40 characters?
unix
seqkit
fasta
updated 20 days ago by
Roop
• 0 • written 21 days ago by
fishingline37
• 0
0
votes
2
replies
1.1k
views
Runtime parameters request: average read/write speed & average total run time
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 7.0 years ago by
tantrev
▴ 30
10
votes
9
replies
1.1k
views
Help interpretating DESeq2 output
Deseq2
Fold-Change
RNA-seq
updated 11 days ago by
Ram
40k • written 2.8 years ago by
nanoide
▴ 100
0
votes
1
reply
1.0k
views
Downstream analysis on multi-sample or single-sample VCF files?
next-gen
VCF
updated 11 days ago by
Ram
40k • written 2.8 years ago by
NGSCanBioinf
▴ 10
2
votes
4
replies
1.0k
views
How to convert Seurat object to sce object retaining the HVG
HVG
single-cell
SingleCellExperiment
seurat
updated 20 days ago by
Hamid Ghaedi
3.0k • written 7 months ago by
paria
▴ 70
0
votes
2
replies
1.0k
views
Error with galGal6 genome
karyoploter
R
karyoploteR
updated 26 days ago by
bernatgel
★ 3.4k • written 3.4 years ago by
palabari
▴ 10
3
votes
5
replies
1.0k
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio
purge_dups
Assembly
bionano
updated 12 days ago by
colindaven
5.5k • written 2.6 years ago by
pablo
▴ 280
3
votes
2
replies
1.0k
views
Contradiction in Harzard ratio and Log fold change
LogFC
Fold-change
Cancer
Hazard-Ratio
HR
updated 11 days ago by
Ram
40k • written 2.4 years ago by
Amir.Asgary
▴ 30
15
votes
6
replies
998
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
19 hours ago by
Rafael Soler
★ 1.2k
4
votes
3
replies
997
views
INSTALLING DEseq2 via conda
DEseq2
conda
RNA-seq
updated 7 days ago by
Ram
40k • written 4 months ago by
Fizzah
▴ 30
0
votes
9
replies
996
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 14 hours ago by
rfran010
▴ 810 • written 12 days ago by
pb11
▴ 10
1
vote
1
reply
983
views
SCENIC-openloom not working
sc-rna
SCENIC
sequencing
updated 1 day ago by
kyriakds
• 0 • written 2.1 years ago by
Lekshmy
▴ 10
1
vote
5
replies
954
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx
differential-expression
t-test
deconvolution
14 days ago by
Sam
▴ 290
0
votes
6
replies
951
views
How to run delly with multi-threading mode?
SV
calling
delly
updated 7 days ago by
bio-jr
▴ 10 • written 8 months ago by
Xi
• 0
0
votes
7
replies
916
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 14 hours ago by
rfran010
▴ 810 • written 13 days ago by
ccbb7aab4
▴ 20
0
votes
2
replies
908
views
STAR-FUSION error
STAR-FUSION
CTAT
updated 1 day ago by
Ram
40k • written 14 months ago by
mc123
• 0
11
votes
4
replies
908
views
How to determine % similarity between genomes?
mauve
mugsy
genome-alignment
updated 5 days ago by
Ram
40k • written 2.5 years ago by
A_heath
▴ 140
0
votes
1
reply
904
views
Issue interpreting plasmidSPAdes output
plasmidSPAdes
updated 5 days ago by
Ram
40k • written 2.9 years ago by
A_heath
▴ 140
1
vote
10
replies
898
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 4 days ago by
jeffhsu3
• 0 • written 12 weeks ago by
fra.silvestro99
▴ 10
1
vote
2
replies
892
views
Error executing process > consensus_classification in NanoCLUST
Nanoclust
Nanoporesequence
16SrRNA
updated 8 days ago by
Ram
40k • written 18 months ago by
yeshirata
▴ 20
785 results • Page
3 of 16
Recent Votes
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Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Comment: Which function is best for pathway analysis?
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▴ 40
@chris Please look into @Hamid Ghaedi's well documented [post][1] on ORA and GSEA, Or [this][2] documentation. Hope this helps. [1]: ht…
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This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis?
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Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
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• 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject
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It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
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Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
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Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
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by
Istvan Albert
98k
yes correct you have to pass the full prefix and not the directory
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★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
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Comment: Low Alignment rate
by
Mehwish
• 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
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