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783 results • Page
2 of 16
Sort: Views
Rank
Views
Votes
Replies
7
votes
6
replies
3.2k
views
CWL: word counting
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 6.3 years ago by
gultagr
▴ 10
10
votes
18
replies
3.1k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 25 days ago by
Ram
40k • written 15 months ago by
reany
▴ 50
0
votes
1
reply
2.9k
views
PSMC plot (Effective population size)
next-gen
updated 26 days ago by
1601693223
• 0 • written 7.9 years ago by
vicky
▴ 30
8
votes
2
replies
2.9k
views
How to edit fasta headers to keep only ID and organism?
fasta
updated 5 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
4
votes
4
replies
2.9k
views
How to keep the top hits only in the output file of hmmscan?
hmmer
hmmscan
updated 5 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
60
votes
21
replies
2.9k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome
assembly
updated 25 days ago by
Michael
53k • written 26 days ago by
sqshigg
▴ 60
0
votes
1
reply
2.8k
views
RNA-seq compare FPKM's or fold change of different organisms
gene-expression
FPKM
RNA-seq
fold-change
updated 11 days ago by
Ram
40k • written 6.1 years ago by
jehu
▴ 30
3
votes
1
reply
2.8k
views
CWL bwa create index to bwa mem alignment workflow
Common-Workflow-Language
CWL
updated 15 days ago by
Ram
40k • written 6.1 years ago by
Biowoogles
▴ 20
5
votes
4
replies
2.7k
views
Distance Tree For Gerp
conservation
phylogeny
updated 12 days ago by
Diana
• 0 • written 11.7 years ago by
Darked89
4.4k
5
votes
8
replies
2.7k
views
Difference between total number of reads in fastq file and no of bases/nt sequences in fastq file?
FASTQ
updated 7 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
2
votes
2
replies
2.7k
views
Tools to create flanking sequences for variants based on a VCF file and reference genome.
vcf
assay
updated 13 days ago by
estpallag
▴ 10 • written 7.2 years ago by
William
★ 5.2k
0
votes
7
replies
2.7k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 11 days ago by
Ram
40k • written 5.3 years ago by
AP
▴ 80
4
votes
6
replies
2.6k
views
IDT vs primer 3 - PCR dimerisation
PCR
primer3
IDT
primer
updated 11 days ago by
Emrah
• 0 • written 3.1 years ago by
timothy.kirkwood
▴ 130
2
votes
7
replies
2.6k
views
CWL: Getting output file of a CommandLineTool using glob
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 5.2 years ago by
skanwal
▴ 50
8
votes
7
replies
2.4k
views
6 follow
LncRNA Differential Expression and Analysis of lncRNA and mRNA co-expression.
RNA-Seq
alignment
co-expression
lncRNA
DESeq2
updated 25 days ago by
AS-git
• 0 • written 5.0 years ago by
conor93
▴ 70
5
votes
2
replies
2.4k
views
CWL: Comments in Common Workflow Language
Common-Workflow-Language
cwl
updated 14 days ago by
Ram
40k • written 6.4 years ago by
kevin.o.oluoch
▴ 70
1
vote
1
reply
2.4k
views
SNPhylo Error Help: there is no SNP and Na/NaN arguement
snphylo
tree
VCF
phylogenetic
updated 21 days ago by
GenoMax
134k • written 7.1 years ago by
N Smith
▴ 10
8
votes
7
replies
2.3k
views
CWL rerunning completed output
Common-Workflow-Language
CWL
updated 15 days ago by
Ram
40k • written 6.1 years ago by
bruce.moran
▴ 950
1
vote
1
reply
2.3k
views
CWL: Linker error doing 'pip install cwlref-runner' on CentOS 6 system
cwl
centos6
centos
Common-Workflow-Language
pip
updated 14 days ago by
Ram
40k • written 6.3 years ago by
Kevin Ernst
• 0
4
votes
2
replies
2.3k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 21 days ago by
GenoMax
134k • written 3.4 years ago by
ATpoint
76k
2
votes
1
reply
2.3k
views
CWL: Arguments vs Inputs in CommandLineTool.
Common-Workflow-Language
CWL
updated 15 days ago by
Ram
40k • written 5.9 years ago by
mkher
▴ 50
3
votes
10
replies
2.3k
views
Salmon alignment based quantification
Salmon
rna-seq
quantification
updated 4 days ago by
Mat
▴ 60 • written 18 months ago by
biology_inform
▴ 40
1
vote
12
replies
2.2k
views
Confused about % of mapped and unmapped reads output from STAR aligner
RNAseq
STAR
updated 12 days ago by
Ram
40k • written 11 months ago by
mohsamir2016
▴ 30
3
votes
3
replies
2.2k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 4 hours ago by
Ram
40k • written 2.0 years ago by
Anand
▴ 40
3
votes
7
replies
2.1k
views
Corrupted FASTq files with missing "+" under some sequences.
fastq
RNAseq
corruption
recover
updated 17 days ago by
Tommaso
• 0 • written 2.4 years ago by
akh22
▴ 90
75
votes
18
replies
2.1k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 7 days ago by
Ram
40k • written 12 days ago by
Kenny
▴ 30
5
votes
8
replies
2.0k
views
Distinguish between forward strand, plus strand, sense strand
pysam
strand
star
sam
updated 22 days ago by
Buwei
• 0 • written 14 months ago by
tien
▴ 10
2
votes
7
replies
2.0k
views
PLINK --geno and --mind
PLINK
COVID-19
updated 20 days ago by
karthivalarmathi99
▴ 10 • written 8 months ago by
Ryon
• 0
0
votes
3
replies
2.0k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 6 days ago by
aishwarya
• 0 • written 5.2 years ago by
blooming.daisy333
▴ 110
6
votes
4
replies
2.0k
views
CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
Common-Workflow-Language
CWL
updated 15 days ago by
Ram
40k • written 4.0 years ago by
skanwal
▴ 50
1
vote
4
replies
2.0k
views
Using ExomeDepth for GRCH38 processed samples to call CNVs
Exome
GrCh38
ExomeDepth
CNV
updated 7 days ago by
Joel Wallenius
▴ 180 • written 2.6 years ago by
nkausthu
▴ 30
2
votes
7
replies
2.0k
views
Issues Phasing with Eagle v2.4
h19
vcf
phasing
eaglev2.4
haplotype
updated 28 days ago by
Robert
• 0 • written 20 months ago by
Francisco
• 0
0
votes
2
replies
1.9k
views
CWL :File created on fly by one step of a workflow as input to another step
Common-Workflow-Language
CWL
updated 14 days ago by
Ram
40k • written 6.5 years ago by
akashmdr90
• 0
4
votes
1
reply
1.9k
views
How to convert File to array of File? Type mismatch between source and sink, File to array
Common-Workflow-Language
cwl
updated 14 days ago by
Ram
40k • written 6.9 years ago by
karl.nordstrom
▴ 90
1
vote
2
replies
1.9k
views
bcftools merge is resulting in a lot of missing data, how do I fix this?
vcf
bcf
updated 14 days ago by
r.shamsi
• 0 • written 2.4 years ago by
devenvyas
▴ 730
7
votes
4
replies
1.9k
views
Structural variant breakend
structural-variant
updated 5 days ago by
Ram
40k • written 2.1 years ago by
A_heath
▴ 140
23
votes
12
replies
1.9k
views
Genes encoded on both strands of DNA?
Genes
strand
updated 5 days ago by
Ram
40k • written 17 months ago by
A_heath
▴ 140
3
votes
15
replies
1.9k
views
9 follow
Help writing code for a question on my homework
biopython
updated 1 day ago by
Andreas
• 0 • written 2.4 years ago by
hannahcheyenna
• 0
2
votes
5
replies
1.8k
views
6 follow
Samtools Failing to Install through Conda
samtools
conda
updated 5 hours ago by
Ram
40k • written 17 months ago by
jjp55
▴ 20
8
votes
14
replies
1.8k
views
How to remove fasta headers in a multifasta file and write file name as a fasta header?
gene
sequence
genome
alignment
next-gen
updated 18 days ago by
Joe
21k • written 3.0 years ago by
Kumar
▴ 120
16
votes
16
replies
1.8k
views
Species identifcation using 16s rRNA
16srRNA
fasta
updated 5 days ago by
Ram
40k • written 2.6 years ago by
A_heath
▴ 140
2
votes
5
replies
1.8k
views
How to make alpha diversity boxplot?
alpha_diversity
taxa
ASV
box_plot
shannon
updated 1 day ago by
yeah
• 0 • written 10 months ago by
Amr
▴ 140
3
votes
2
replies
1.7k
views
Extracting Residuals from Differential Expression Model
statistics
residuals
limma
updated 19 days ago by
Gordon Smyth
★ 6.4k • written 4.2 years ago by
JourneyToAbyss
▴ 210
3
votes
2
replies
1.7k
views
Problems drawing cytobands with karyoploteR
RNA-Seq
R
Bioconductor
updated 26 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 1 day 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 13 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 22 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 15 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 14 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 5 days ago by
Ram
40k • written 24 months ago by
A_heath
▴ 140
783 results • Page
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Comment: Violin plot (Monocle 3) - Troubleshooting
by
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I see the error message but I'm confused on what it's telling me.
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Comment: How to plot proportion of cells in each cluster with scanpy?
by
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▴ 110
Thank you for replying again. The "type" still causes issues but the reply by Radu Tanasa worked.
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Thank you so much. That worked perfectly and it was much faster than what I was trying.
Answer: How to plot proportion of cells in each cluster with scanpy?
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Hi. If I get this right, you simply need to compute the percentage of cells in each cluster at the dataset level? ```py import pandas as p…
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Why would that be an advantage?
Comment: How to plot proportion of cells in each cluster with scanpy?
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The following code will write percentage in your stacked barplot. cross_tab = pd.crosstab(adata.obs['leiden_0.6'],adata.obs['typ…
Comment: How to check RNAseq support for annotated genes?
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@juke34 Thanks for the suggestion. I wonder if bedtool coverage or intersect can be used to check the transcript support or coverage for ea…
Comment: How to plot proportion of cells in each cluster with scanpy?
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Because that was the code from the link. It is how they specified they had 2 groups of samples but I don't have 2 groups. Sorry for the con…
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by
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★ 1.2k
No there is no bug in this. Please see carefully what the `error` message tells to you.
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@michaeld Thanks. I tried it using STAR to map the transcript to the annotation gtf file, and was planning to use featureCounts/gene Counts…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bk11
★ 1.2k
Why you had `type` in your code above then?
Comment: Comparing multiple columns from two files using AWK
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40k
R's dplyr will serve well here. ```r fileA %>% mutate(V3 = sub(V3, "chr","") %>% inner_join(fileB, join_by(V3 == chr, window_end <= V4, ..…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Thank you for the suggestion. Unfortunately, that does not work for me because I do not have a "type" argument in the adata.obs. I think th…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
• 0
I'm still seeing errors: First I tried the code you mentioned except I use `clusters` instead of `embryo.time.bin` since this is a column…
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