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779 results • Page
3 of 16
Sort: Views
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Views
Votes
Replies
3
votes
2
replies
1.7k
views
Problems drawing cytobands with karyoploteR
RNA-Seq
R
Bioconductor
updated 29 days ago by
bernatgel
★ 3.4k • written 4.5 years ago by
uxiavb
▴ 10
0
votes
1
reply
1.7k
views
error when running local chlorop1.1
chlorop
updated 4 days ago by
Ram
40k • written 7.3 years ago by
gerrychang1985
▴ 40
7
votes
8
replies
1.7k
views
7 follow
what is the mean of the file "*._f1.fq.gz" and "*._r2.fa.gz"
RNA-Seq
updated 17 days ago by
yhdist
▴ 70 • written 3.4 years ago by
yueli7
▴ 250
1
vote
2
replies
1.6k
views
junction_annotation.py: How many 'novel' splice junctions/splice events are resonably expected from human RNA,
RNA-Seq
junction_annotation.py
human
updated 25 days ago by
Nicolas Lichilin
▴ 20 • written 4.6 years ago by
RNAseqer
▴ 250
1
vote
1
reply
1.6k
views
make paths variable in .cwl workflows and corresponding -job files
Common-Workflow-Language
cwl
updated 18 days ago by
Ram
40k • written 7.0 years ago by
c.ravarani
• 0
1
vote
5
replies
1.6k
views
Failing to use $mixin to include "global" settings
Common-Workflow-Language
cwl
updated 18 days ago by
Ram
40k • written 6.9 years ago by
karl.nordstrom
▴ 90
8
votes
5
replies
1.6k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 8 days ago by
Ram
40k • written 24 months ago by
A_heath
▴ 140
2
votes
20
replies
1.6k
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
23 days ago by
Maxine
▴ 30
0
votes
2
replies
1.6k
views
Question about REDItools
REDItools
updated 14 days ago by
Ethan Lee
• 0 • written 4.1 years ago by
tujuchuanli
▴ 100
3
votes
4
replies
1.5k
views
Reference implementation rejects step without inputs
Common-Workflow-Language
cwl
updated 18 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 18 days ago by
Ram
40k • written 4.4 years ago by
mavrommatis.konstantinos
▴ 10
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 3 days ago by
Ram
40k • written 6 weeks ago by
epianalysis
• 0
0
votes
7
replies
1.5k
views
what does "total read count" means in fastqc file. how does it helpful for analysis
fastqc
updated 10 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 7 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 8 days ago by
Ram
40k • written 2.1 years ago by
A_heath
▴ 140
2
votes
2
replies
1.5k
views
CWL : default value and label for argument
Common-Workflow-Language
cwl
updated 18 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 18 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 25 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 10 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 24 days ago by
Ram
40k • written 2.1 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 18 days ago by
Ram
40k • written 7.0 years ago by
c.ravarani
• 0
4
votes
12
replies
1.3k
views
Does anyone know how to download genBlastG?
gene-finding
genBlastG
updated 2 days ago by
dukecomeback
▴ 40 • written 5 months ago by
jaredbernard
▴ 20
0
votes
2
replies
1.3k
views
Converting hdf5 file to loom file
single-cell
python
scvelo
RNA
updated 1 day ago by
bk11
★ 1.3k • written 2.4 years ago by
sidrah.maryam
▴ 50
2
votes
4
replies
1.3k
views
How to get mm39 repeatmasker track from UCSC genome browser
genome
ucsc
updated 21 days ago by
bioinfo_wen
▴ 10 • written 22 months ago by
saarantras
▴ 20
1
vote
5
replies
1.3k
views
Unmapped Reads in Kallisto
Kallisto
RNA-Seq
alignment
bustools
updated 1 day ago by
dsull
★ 4.8k • written 3.6 years ago by
msutennis23
• 0
0
votes
3
replies
1.3k
views
how to calculate BAF and LRR from VCF or BCF files?
SNP
BAF
LRR
Variation
9 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 10 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 17 days ago by
ATpoint
77k • written 10 months ago by
dlaehnemann
▴ 30
3
votes
1
reply
1.2k
views
%% error in Rstudio
seurat
r
updated 7 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 18 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 8 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 10 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
28 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
21 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 8 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 24 days ago by
karthivalarmathi99
▴ 10 • written 2.2 years ago by
Emy
▴ 50
8
votes
17
replies
1.1k
views
7 follow
How to limit fasta header to 40 characters?
unix
seqkit
fasta
updated 23 days ago by
Roop
• 0 • written 24 days ago by
fishingline37
• 0
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 25 days ago by
e.r.zakiev
▴ 80 • written 3.1 years ago by
Melinda
• 0
9
votes
4
replies
1.1k
views
Illumina Q score
Illumina
quality-score
updated 8 days ago by
Ram
40k • written 2.1 years ago by
A_heath
▴ 140
0
votes
2
replies
1.1k
views
Runtime parameters request: average read/write speed & average total run time
Common-Workflow-Language
cwl
updated 18 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 14 days ago by
Ram
40k • written 2.8 years ago by
nanoide
▴ 110
0
votes
1
reply
1.0k
views
Downstream analysis on multi-sample or single-sample VCF files?
next-gen
VCF
updated 14 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 23 days ago by
Hamid Ghaedi
3.0k • written 7 months ago by
paria
▴ 70
0
votes
9
replies
1.0k
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 3 days ago by
rfran010
▴ 830 • written 15 days ago by
pb11
▴ 10
0
votes
2
replies
1.0k
views
Error with galGal6 genome
karyoploter
R
karyoploteR
updated 29 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 16 days ago by
colindaven
5.5k • written 2.7 years ago by
pablo
▴ 280
15
votes
6
replies
1.0k
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
4 days ago by
Rafael Soler
★ 1.2k
4
votes
3
replies
1.0k
views
INSTALLING DEseq2 via conda
DEseq2
conda
RNA-seq
updated 10 days ago by
Ram
40k • written 4 months ago by
Fizzah
▴ 30
3
votes
2
replies
1.0k
views
Contradiction in Harzard ratio and Log fold change
LogFC
Fold-change
Cancer
Hazard-Ratio
HR
updated 14 days ago by
Ram
40k • written 2.5 years ago by
Amir.Asgary
▴ 30
1
vote
1
reply
994
views
SCENIC-openloom not working
sc-rna
SCENIC
sequencing
updated 5 days ago by
kyriakds
• 0 • written 2.1 years ago by
Lekshmy
▴ 10
779 results • Page
3 of 16
Recent Votes
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
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Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
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157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
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I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
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157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
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I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
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77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
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by
fifty_fifty
▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Ram
40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools
by
Amitm
★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
This is a really neat package, but I don't think it does exactly what I want, so I've clarified my question. This seems like it grabs a PD…
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