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778 results • Page
1 of 16
Sort: replies
Rank
Views
Votes
Replies
298
votes
122
replies
28k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 25 days ago by
jena
▴ 270 • written 13.2 years ago by
Eric Normandeau
11k
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 11 days ago by
rohitsatyam102
▴ 750 • written 12.5 years ago by
Ketil
4.1k
121
votes
55
replies
95k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 3 days ago by
jl19
• 0 • written 9.3 years ago by
kay
▴ 340
84
votes
47
replies
30k
views
28 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 2 days ago by
Ram
40k • written 10.0 years ago by
Irsan
★ 7.7k
170
votes
41
replies
92k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 7 days ago by
Ram
40k • written 12.3 years ago by
Palu
▴ 250
100
votes
38
replies
29k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 1 day ago by
Jeremy Leipzig
21k • written 9.9 years ago by
14134125465346445
★ 3.6k
100
votes
33
replies
105k
views
23 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 2 days ago by
ella
• 0 • written 11.3 years ago by
GPR
▴ 390
105
votes
26
replies
40k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 12 days ago by
zx8754
11k • written 10.7 years ago by
henryvuong
▴ 810
38
votes
25
replies
8.1k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 17 days ago by
Ram
40k • written 7.5 years ago by
waqasnayab
▴ 250
36
votes
23
replies
27k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 28 days ago by
s.w.vanderlaan
▴ 40 • written 2.2 years ago by
Michal Nevo
▴ 110
33
votes
23
replies
18k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq
genome
updated 16 days ago by
alejandrogzi
▴ 30 • written 5.5 years ago by
JJ
▴ 660
18
votes
22
replies
8.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 7 days ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
81
votes
21
replies
40k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 15 days ago by
Joel Wallenius
▴ 180 • written 9.6 years ago by
pristanna
▴ 750
60
votes
21
replies
2.9k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome
assembly
updated 28 days ago by
Michael
53k • written 4 weeks ago by
sqshigg
▴ 60
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
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 11 days ago by
Ram
40k • written 15 days ago by
Kenny
▴ 30
10
votes
18
replies
3.2k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 29 days ago by
Ram
40k • written 15 months ago by
reany
▴ 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
16
votes
16
replies
1.8k
views
Species identifcation using 16s rRNA
16srRNA
fasta
updated 8 days ago by
Ram
40k • written 2.6 years ago by
A_heath
▴ 140
15
votes
16
replies
721
views
ncbi error report log for validate fastq issue
sra-tools
updated 2 days ago by
GenoMax
134k • written 3 days ago by
1769mkc
★ 1.1k
36
votes
16
replies
28k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 10 days ago by
jkbonfield
★ 1.1k • written 4.6 years ago by
chparada
▴ 60
7
votes
15
replies
3.3k
views
Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index
next-gen
sequencing
updated 11 days ago by
Gabriel R.
★ 2.9k • written 3.3 years ago by
Rezenman
• 0
3
votes
15
replies
463
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
1 day ago by
ella
• 0
3
votes
14
replies
1.9k
views
10 follow
Help writing code for a question on my homework
biopython
updated 3 days ago by
Joe
21k • written 2.4 years ago by
hannahcheyenna
• 0
19
votes
14
replies
927
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 9 days ago by
Jeremy Leipzig
21k • written 10 days ago by
vincenthus
▴ 70
8
votes
14
replies
1.9k
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 21 days ago by
Joe
21k • written 3.0 years ago by
Kumar
▴ 120
10
votes
13
replies
12k
views
6 follow
How to annotate only selected genes on a heatmap
R
updated 25 days ago by
GenoMax
134k • written 6.3 years ago by
h.fushimi.x689
▴ 30
49
votes
13
replies
52k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 2 days ago by
camillab.
▴ 140 • written 7.7 years ago by
nash.claire
▴ 490
7
votes
13
replies
751
views
Help with Error: Required version of NumPy not available: installation of Numpy >= 1.6 not found
seurat
leiden
29 days ago by
Chris
▴ 200
0
votes
13
replies
588
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
6 days ago by
Y
• 0
0
votes
13
replies
700
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn
Trinity
Transcriptome
RNA-seq-analysis
De-novo-transcriptome-assembly
7 days ago by
langziv
▴ 50
19
votes
13
replies
6.8k
views
9 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 23 hours ago by
dariober
14k • written 15 months ago by
ATpoint
77k
124
votes
13
replies
166k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 24 days ago by
Ram
40k • written 13.2 years ago by
Biomed
4.9k
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
4
votes
12
replies
3.4k
views
6 follow
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 17 days ago by
alejandrogzi
▴ 30 • written 3.4 years ago by
William
★ 5.2k
4
votes
12
replies
875
views
bedops alternative for bedtools -unionbedg ?
bedtools
bam
coverage
bedops
bed
updated 14 days ago by
Alex Reynolds
35k • written 4 weeks ago by
Agastya
▴ 10
1
vote
12
replies
2.2k
views
Confused about % of mapped and unmapped reads output from STAR aligner
RNAseq
STAR
updated 15 days ago by
Ram
40k • written 11 months ago by
mohsamir2016
▴ 30
23
votes
12
replies
1.9k
views
Genes encoded on both strands of DNA?
Genes
strand
updated 8 days ago by
Ram
40k • written 17 months ago by
A_heath
▴ 140
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
9
votes
12
replies
4.2k
views
converting a list of genes and interaction to a graph
gene
R
updated 9 days ago by
Amirhossein Hajianpour
▴ 40 • written 7.7 years ago by
fi1d18
★ 4.2k
13
votes
12
replies
32k
views
Estimating Insert Size From Paired End Data.
picard
alignment
paired-end
updated 2 days ago by
Ram
40k • written 9.6 years ago by
GouthamAtla
12k
5
votes
12
replies
848
views
Converting custom VCF to standard VCF
VCF
15 days ago by
avelarbio46
▴ 30
2
votes
11
replies
880
views
Extracting regions around sites in VCF file and writing them as fasta sequences/files
VCF
fasta
updated 17 days ago by
GenoMax
134k • written 4 weeks ago by
Aiswarya
▴ 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
1
vote
11
replies
789
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 5 days ago by
GenoMax
134k • written 4 weeks ago by
langziv
▴ 50
0
votes
11
replies
750
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
9 days ago by
evmae
• 0
1
vote
10
replies
915
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 7 days ago by
jeffhsu3
• 0 • written 12 weeks ago by
fra.silvestro99
▴ 10
3
votes
10
replies
526
views
STAR index not working
STAR
RNA-Seq
8 days ago by
camillab.
▴ 140
19
votes
10
replies
896
views
Forum:
Pain points using commercial clouds
gpt
tinybio
updated 15 days ago by
vincenthus
▴ 70 • written 4 weeks ago by
Sasha
▴ 720
7
votes
10
replies
528
views
Batch effect normalization
RNA-seq
batch-effect
updated 11 days ago by
Ram
40k • written 12 days ago by
Smriti
• 0
778 results • Page
1 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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Recent Replies
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
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
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
by
langziv
▴ 50
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
by
Pierre Lindenbaum
157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data
by
fifty_fifty
▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Ram
40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools
by
Amitm
★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${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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