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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
8
votes
20
replies
2.5k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
5.7 years ago by
corend
▴ 70
6
votes
20
replies
5.9k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.3 years ago by
princy149
▴ 80
22
votes
20
replies
2.2k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 5 months ago by
Ram
40k • written 7.2 years ago by
Farbod
★ 3.4k
9
votes
20
replies
3.6k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 6 months ago by
Ram
40k • written 5.1 years ago by
marongiu.luigi
▴ 690
5
votes
20
replies
3.6k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 12 months ago by
Ram
40k • written 8.1 years ago by
Hans
▴ 140
8
votes
20
replies
2.2k
views
Getting read depth for normal and tumour
R
WGS
vcf
4.5 years ago by
fi1d18
★ 4.2k
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
19 days ago by
Maxine
▴ 30
8
votes
20
replies
2.0k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 16 months ago by
Ram
40k • written 5.2 years ago by
Bara'a
▴ 270
5
votes
20
replies
7.8k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.1 years ago by
varsha619
▴ 90
4
votes
20
replies
1.5k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
3.7 years ago by
schlogl
▴ 150
6
votes
19
replies
2.4k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
4.2 years ago by
aloke205
▴ 40
7
votes
19
replies
2.6k
views
mapping script process sleeping on server.
alignment
updated 16 months ago by
Ram
40k • written 8.6 years ago by
lvogel
▴ 30
15
votes
19
replies
1.6k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.4 years ago by
Ram
40k • written 5.4 years ago by
Nadin.asal
• 0
9
votes
19
replies
1.9k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.7 years ago by
schlogl
▴ 150
4
votes
19
replies
2.7k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 6.1 years ago by
Biostar
20 • written 6.2 years ago by
cool.abbecker
▴ 30
17
votes
19
replies
2.4k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.1 years ago by
Gian77
▴ 60
10
votes
19
replies
2.8k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.4 years ago by
GenoMax
134k • written 2.4 years ago by
matt
▴ 20
1
vote
19
replies
6.3k
views
Conda install package - different internals
R
software error
updated 4.1 years ago by
Biostar
20 • written 4.1 years ago by
lihe.liu
▴ 30
0
votes
19
replies
2.4k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
2.1 years ago by
rheab1230
▴ 140
0
votes
19
replies
3.5k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
5.7 years ago by
jaqx008
▴ 110
7
votes
19
replies
6.6k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 20 months ago by
Ram
40k • written 8.9 years ago by
mheiser1
▴ 10
0
votes
19
replies
1.2k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
3.8 years ago by
marongiu.luigi
▴ 690
1
vote
19
replies
1.7k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
4.8 years ago by
eozcan
▴ 10
3
votes
19
replies
5.3k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 4.4 years ago by
finswimmer
16k • written 4.4 years ago by
sruthi
▴ 40
6
votes
19
replies
1.4k
views
Fastq header modification
sequence
next-gen
updated 5.5 years ago by
Ram
40k • written 5.5 years ago by
Guillaume
• 0
13
votes
19
replies
4.8k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.8 years ago by
bioplanet
▴ 60
18
votes
19
replies
1.9k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 9 months ago by
Ram
40k • written 4.7 years ago by
rbkh09
• 0
22
votes
19
replies
2.7k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.0 years ago by
fi1d18
★ 4.2k
5
votes
19
replies
1.4k
views
how I can come up with a permanent error
R
software error
6.4 years ago by
fi1d18
★ 4.2k
0
votes
19
replies
8.9k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.3 years ago by
seta
★ 1.8k
0
votes
19
replies
1.5k
views
scatterplot in R
microarray
expression
gene
updated 11 months ago by
Ram
40k • written 11 months ago by
bioinformatics
▴ 20
3
votes
19
replies
867
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 12 weeks ago by
Asaf
10k • written 12 weeks ago by
captainlabman
• 0
0
votes
19
replies
1.2k
views
map fasts files
RNA-Seq
FASTQ
R
5.6 years ago by
Learner
▴ 270
2
votes
18
replies
5.7k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
6.9 years ago by
Sumit Paliwal
▴ 40
0
votes
18
replies
1.2k
views
No gene name after annovar vcf file processing
vcf
annovar
4.0 years ago by
valerie
▴ 100
7
votes
18
replies
8.0k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 19 months ago by
Ram
40k • written 8.9 years ago by
hana
▴ 190
16
votes
18
replies
4.7k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.1 years ago by
Mensur Dlakic
★ 25k • written 4.1 years ago by
tikshyadav19
• 0
1
vote
18
replies
1.4k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 4.1 years ago by
Biostar
20 • written 4.1 years ago by
Natasha
▴ 40
2
votes
18
replies
2.0k
views
I need help in this
gene
weblems
alignment
updated 13 months ago by
Ram
40k • written 7.8 years ago by
efosa15
• 0
3
votes
18
replies
1.4k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
11 months ago by
lacb
▴ 120
4
votes
18
replies
14k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 2.9 years ago by
Biostar
20 • written 5.1 years ago by
Shelle
▴ 30
0
votes
18
replies
1.5k
views
freebayes error variant calling
snp
3.1 years ago by
evelyn
▴ 220
5
votes
18
replies
5.8k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
3.8 years ago by
michelle.piquet
▴ 60
14
votes
18
replies
4.5k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.7 years ago by
Biostar
20 • written 6.9 years ago by
plink_9857
▴ 50
3
votes
18
replies
2.5k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 2.2 years ago by
Ram
40k • written 2.2 years ago by
Nai
▴ 50
7
votes
18
replies
4.4k
views
Fold change UP and Down in dplyr calculation
R
6.1 years ago by
1769mkc
★ 1.1k
4
votes
18
replies
3.6k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 13 months ago by
Ram
40k • written 7.8 years ago by
Joel TM
▴ 60
2
votes
18
replies
2.2k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
20 months ago by
shivangi.agarwal800
▴ 120
0
votes
18
replies
1.1k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 4 weeks ago by
GenoMax
134k • written 4 weeks ago by
Apex92
▴ 270
1
vote
18
replies
2.3k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
7.2 years ago by
Tom
▴ 40
1,000 results • Page
2 of 20
Recent Votes
Answer: How to plot proportion of cells in each cluster with scanpy?
Comment: How the first sequencing product removed in pair end sequencing
Comment: WGCNA Labeled Heatmap
C: Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
Comment: Hisat2 index and alignment question
A: Finding overlaps between GRanges objects
A: Finding overlaps between GRanges objects
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Recent Replies
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 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: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
• 0
I'm still stuck on how to fix this.
Answer: How to plot proportion of cells in each cluster with scanpy?
by
Radu Tanasa
▴ 60
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…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
Why would that be an advantage?
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bk11
★ 1.2k
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?
by
BioinfoBee
• 0
@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?
by
bioinfo
▴ 110
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…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
bk11
★ 1.2k
No there is no bug in this. Please see carefully what the `error` message tells to you.
Comment: How to check RNAseq support for annotated genes?
by
BioinfoBee
• 0
@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
by
Ram
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…
Comment: Comparing multiple columns from two files using AWK
by
emiliomastriani
▴ 30
Thank you for the formatting support. Please, can you suggest the code (R/Python) to approach my problem? Something I can use as a starting…
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