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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
11
votes
42
replies
3.4k
views
over presented kmer in fastq
fastqc
RNA-Seq
6.0 years ago by
Sam
▴ 150
28
votes
42
replies
6.2k
views
7 follow
How to add tophat and bowtie to the path?
export PATH
bowtie2.2.9
tophat2
6.8 years ago by
mirza
▴ 180
122
votes
42
replies
9.4k
views
21 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta
biostars
updated 7 months ago by
Ram
40k • written 10.8 years ago by
Istvan Albert
98k
8
votes
42
replies
4.1k
views
NaS (Nanopore Synthetic-long) help
Assembly
preprocessing
updated 8 months ago by
Ram
40k • written 8.3 years ago by
midox
▴ 290
138
votes
42
replies
21k
views
22 follow
Forum:
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 6 months ago by
LauferVA
3.7k • written 10.3 years ago by
Whetting
★ 1.6k
57
votes
42
replies
5.8k
views
12 follow
Forum:
Why is academic software hard to install?
software-installation
updated 20 months ago by
Ram
40k • written 9.0 years ago by
lh3
33k
5
votes
41
replies
2.3k
views
Insert sequence in nt database
nt
3.4 years ago by
anasofiamoreira94
▴ 80
19
votes
41
replies
8.0k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 6.1 years ago by
ivivek_ngs
★ 5.2k • written 6.1 years ago by
sophialovechan
▴ 80
38
votes
41
replies
54k
views
9 follow
Volcano Plot from DEseq2
R
written 5.9 years ago by
1769mkc
★ 1.1k
31
votes
41
replies
2.0k
views
12 follow
Forum:
Question regarding journal publications
publications
journals
updated 3 months ago by
Ram
40k • written 3.6 years ago by
K.Gee
▴ 40
18
votes
41
replies
12k
views
6 follow
paired end illumina reads
Assembly
paired end
updated 14 months ago by
Ram
40k • written 7.9 years ago by
midox
▴ 290
26
votes
41
replies
15k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 10 months ago by
lovelymaoqin
• 0 • written 5.7 years ago by
BrunoGiotti
▴ 120
23
votes
41
replies
3.1k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS
biopython
illumina
WGS
updated 4 months ago by
Ram
40k • written 5 months ago by
Vijith
▴ 30
98
votes
41
replies
5.1k
views
17 follow
Forum:
I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error
next-gen-sequencing
updated 5 months ago by
Ram
40k • written 7.1 years ago by
moxu
▴ 510
203
votes
41
replies
24k
views
20 follow
Forum:
Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics
cram
gatk
galaxy
updated 7 months ago by
Ram
40k • written 8.9 years ago by
William
★ 5.2k
13
votes
41
replies
1.9k
views
Is my file created completely
sam
BWA-MEM
BWA
updated 6 months ago by
Ram
40k • written 6.4 years ago by
micro32uvas
▴ 10
16
votes
41
replies
8.4k
views
How to extract information from headers of fasta file
sequence
updated 15 months ago by
Ram
40k • written 8.5 years ago by
Crystal
▴ 70
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 4 days ago by
Ram
40k • written 12.3 years ago by
Palu
▴ 250
18
votes
40
replies
17k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 6 months ago by
Ram
40k • written 7.2 years ago by
Esaie
▴ 170
6
votes
40
replies
9.8k
views
Fastx_Collapser Has No Fastq Output
fastx
RNA-seq
updated 7 months ago by
Ram
40k • written 10.0 years ago by
nbvasani
▴ 240
10
votes
40
replies
5.6k
views
weird insert size post trimming
RNA-Seq
updated 6.1 years ago by
Gabriel R.
★ 2.9k • written 6.1 years ago by
badribio
▴ 280
68
votes
40
replies
5.4k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen
sequencing
sequencing
updated 11.9 years ago by
pmenzel
▴ 310 • written 11.9 years ago by
Samuel Lampa
★ 1.3k
40
votes
40
replies
10k
views
9 follow
What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
ATAC-seq
alignment
updated 5.6 years ago by
Kevin Blighe
86k • written 7.0 years ago by
datascientist28
▴ 550
67
votes
40
replies
8.7k
views
12 follow
Forum:
I want to re-open the old debate: python or perl ?
perl
python
updated 19 months ago by
Ram
40k • written 8.9 years ago by
Gabriel R.
★ 2.9k
16
votes
40
replies
5.4k
views
About TCGA CNV data preprocessing
SNP
CNV
updated 5.0 years ago by
Kevin Blighe
86k • written 5.0 years ago by
Eric Wang
▴ 40
151
votes
39
replies
23k
views
20 follow
Forum:
A Farewell To Bioinformatics
bioinformatics
updated 7 months ago by
Ram
40k • written 10.7 years ago by
Martin A Hansen
3.0k
20
votes
39
replies
8.6k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast
blast
memory
updated 8.0 years ago by
Kumar
▴ 170 • written 11.7 years ago by
Amr
▴ 160
226
votes
39
replies
284k
views
33 follow
Gene Id Conversion Tool
mapping
conversion
updated 13 months ago by
Ram
40k • written 13.9 years ago by
Renee
▴ 620
25
votes
39
replies
5.0k
views
8 follow
Forum:
Bioinformatics Study Group
study-group
updated 7 months ago by
Ram
40k • written 10.2 years ago by
Olivier
▴ 440
282
votes
39
replies
174k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 6 months ago by
Ram
40k • written 9.1 years ago by
Obi Griffith
20k
55
votes
39
replies
5.0k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf
python
perl
awk
updated 11.1 years ago by
Rm
8.2k • written 11.1 years ago by
Mahdi Sarmady
▴ 310
69
votes
39
replies
3.8k
views
14 follow
Forum:
Preparation for Bioinformatics.SE closing
meta
biostars
updated 4 months ago by
Ram
40k • written 6.3 years ago by
John
13k
11
votes
39
replies
3.4k
views
Any advice for a de novo genome assembly
k-mer
de novo
genome
assembly
updated 6.8 years ago by
krsahlin
▴ 60 • written 6.9 years ago by
Picasa
▴ 640
66
votes
39
replies
6.9k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career
subjective
updated 2.5 years ago by
Ram
40k • written 13.5 years ago by
Marcos De Carvalho
▴ 310
81
votes
39
replies
6.6k
views
11 follow
News:
State Of Biostar - Future Directions (January 2013)
biostars
updated 7 months ago by
Ram
40k • written 10.7 years ago by
Istvan Albert
98k
93
votes
39
replies
142k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by
Dan
▴ 140 • written 11.2 years ago by
abi
▴ 380
36
votes
39
replies
3.2k
views
11 follow
Forum:
Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast
RNA-Seq
alignment
next-gen-sequencing
updated 4 months ago by
Ram
40k • written 5.9 years ago by
dhbradshaw
▴ 130
18
votes
39
replies
3.3k
views
Tool:
CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 4 months ago by
Ram
40k • written 4.5 years ago by
chernouhov sergey
▴ 50
100
votes
38
replies
29k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 27 days ago by
Jeremy Leipzig
21k • written 9.9 years ago by
14134125465346445
★ 3.6k
129
votes
38
replies
6.7k
views
21 follow
Forum:
Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 3 months ago by
Ram
40k • written 4.5 years ago by
Istvan Albert
98k
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 17 months ago by
Ram
40k • written 8.6 years ago by
Mo
▴ 920
229
votes
38
replies
140k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 3 months ago by
Ram
40k • written 10.6 years ago by
Malachi Griffith
19k
48
votes
38
replies
16k
views
8 follow
Forum:
Eukaryotic Genome Annotation in 2016
software
genome
annotation
updated 5 months ago by
Ram
40k • written 7.5 years ago by
Eric Normandeau
11k
39
votes
38
replies
7.7k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 13 months ago by
Ram
40k • written 7.9 years ago by
John
13k
27
votes
38
replies
19k
views
Heatmap based with FPKM values
RNA-Seq
next-gen
R
updated 4.4 years ago by
Biostar
20 • written 5.9 years ago by
Mehmet
▴ 820
53
votes
38
replies
3.8k
views
10 follow
Multiple alignment software
alignment
clustal omega
tcoffee
updated 4.0 years ago by
Istvan Albert
98k • written 4.0 years ago by
juanjo75es
▴ 130
47
votes
37
replies
7.9k
views
12 follow
Forum:
The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 7 months ago by
Ram
40k • written 10.1 years ago by
Niallhaslam
2.3k
29
votes
37
replies
2.9k
views
8 follow
Perl/Python script: phased vcf to phased tped
vcf
ped
phased
4.9 years ago by
Shicheng Guo
★ 9.3k
43
votes
37
replies
1.9k
views
7 follow
Forum:
Checking the quality and reliability in bioinformatics
reproducibility
updated 4 months ago by
Ram
40k • written 6.0 years ago by
fi1d18
★ 4.2k
87
votes
37
replies
49k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 18 months ago by
Ram
40k • written 10.2 years ago by
Hunter
▴ 110
1,000 results • Page
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Comment: Filtering VCF to divide with equal sizes
Answer: How to plot proportion of cells in each cluster with scanpy?
Comment: How the first sequencing product removed in pair end sequencing
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Comment: Hisat2 index and alignment question
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Recent Replies
Comment: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
• 0
I see the error message but I'm confused on what it's telling me.
Answer: Bacterial Pangenome Analysis
by
liorglic
★ 1.2k
I am not sure I understand why you think there is a problem with your analysis. It makes perfect sense that different blastp cutoffs produc…
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: 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…
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