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785 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 22 days ago by
jena
▴ 270 • written 13.2 years ago by
Eric Normandeau
11k
146
votes
70
replies
46k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 29 days ago by
Raheleh
▴ 260 • written 5.8 years ago by
Kevin Blighe
86k
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 7 days ago by
rohitsatyam102
▴ 750 • written 12.5 years ago by
Ketil
4.1k
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
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
105
votes
26
replies
40k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 8 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 14 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 25 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 13 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 4 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 12 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 25 days ago by
Michael
53k • written 26 days ago by
sqshigg
▴ 60
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
20 days ago by
Maxine
▴ 30
10
votes
18
replies
3.1k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 26 days ago by
Ram
40k • written 15 months ago by
reany
▴ 50
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 8 days ago by
Ram
40k • written 12 days ago by
Kenny
▴ 30
8
votes
17
replies
1.1k
views
7 follow
How to limit fasta header to 40 characters?
unix
seqkit
fasta
updated 20 days ago by
Roop
• 0 • written 21 days ago by
fishingline37
• 0
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
36
votes
16
replies
28k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 7 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 7 days ago by
Gabriel R.
★ 2.9k • written 3.3 years ago by
Rezenman
• 0
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
19
votes
14
replies
876
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 6 days ago by
Jeremy Leipzig
21k • written 7 days ago by
vincenthus
▴ 70
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
0
votes
13
replies
663
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn
Trinity
Transcriptome
RNA-seq-analysis
De-novo-transcriptome-assembly
4 days ago by
langziv
▴ 50
124
votes
13
replies
165k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 21 days ago by
Ram
40k • written 13.2 years ago by
Biomed
4.9k
13
votes
13
replies
6.5k
views
6 follow
Extract SNPs flanking sequences based on VCF and genome Fasta files
snp
sequence
genome
updated 28 days ago by
LauGuillardin
• 0 • written 5.1 years ago by
Denis
▴ 280
10
votes
13
replies
12k
views
6 follow
How to annotate only selected genes on a heatmap
R
updated 22 days ago by
GenoMax
134k • written 6.3 years ago by
h.fushimi.x689
▴ 30
0
votes
13
replies
560
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
3 days ago by
Y
• 0
7
votes
13
replies
716
views
Help with Error: Required version of NumPy not available: installation of Numpy >= 1.6 not found
seurat
leiden
26 days ago by
Chris
▴ 180
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 13 hours ago by
Ram
40k • written 5 weeks ago by
epianalysis
• 0
9
votes
12
replies
4.2k
views
converting a list of genes and interaction to a graph
gene
R
updated 6 days ago by
Amirhossein Hajianpour
▴ 40 • written 7.7 years ago by
fi1d18
★ 4.2k
4
votes
12
replies
850
views
bedops alternative for bedtools -unionbedg ?
bedtools
bam
coverage
bedops
bed
updated 11 days ago by
Alex Reynolds
35k • written 27 days ago by
Agastya
▴ 10
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
5
votes
12
replies
828
views
Converting custom VCF to standard VCF
VCF
12 days ago by
avelarbio46
▴ 30
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
4
votes
12
replies
3.4k
views
6 follow
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 14 days ago by
alejandrogzi
▴ 30 • written 3.4 years ago by
William
★ 5.2k
1
vote
11
replies
755
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 2 days ago by
GenoMax
134k • written 29 days ago by
langziv
▴ 50
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
18 days ago by
kalavattam
▴ 180
0
votes
11
replies
730
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
6 days ago by
evmae
• 0
2
votes
11
replies
848
views
Extracting regions around sites in VCF file and writing them as fasta sequences/files
VCF
fasta
updated 14 days ago by
GenoMax
134k • written 28 days ago by
Aiswarya
▴ 10
8
votes
10
replies
3.6k
views
Dataset's name in BioMart for S. pombe
S.pombe
BioMart
dataset
updated 1 hour ago by
YUYANG.OON
• 0 • written 9.3 years ago by
Parham
★ 1.6k
13
votes
10
replies
623
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 1 day ago by
ATpoint
76k • written 4 days ago by
MVJ
▴ 10
8
votes
10
replies
720
views
Inflated GWAS test statistic after merging multiple batches of genotype dataset imputed differently
genotype
imputation
gwas
updated 6 days ago by
LauferVA
3.7k • written 7 days ago by
Amy
▴ 20
18
votes
10
replies
14k
views
Could you please explain Fold change, % of change, and log2 fold change (L2FC) to a layment?
gene
RNA-Seq
next-gen
fold-change
updated 11 days ago by
Ram
40k • written 3.9 years ago by
WUSCHEL
▴ 720
7
votes
10
replies
504
views
Batch effect normalization
RNA-seq
batch-effect
updated 8 days ago by
Ram
40k • written 8 days ago by
Smriti
• 0
19
votes
10
replies
29k
views
6 follow
read depth using samtools
depth
samtools
updated 12 days ago by
Sachin
• 0 • written 4.7 years ago by
LimMo
▴ 30
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
6
votes
10
replies
721
views
Making pairwise matrix using ChIP-Seq peak binding matrix in R
R
matrix
binding
Chip-seq
21 days ago by
Ankit
▴ 390
3
votes
10
replies
394
views
Should I Learn Docker to Run Command Line Bioinformatics Tool?
Docker
updated 10 hours ago by
ATpoint
76k • written 1 day ago by
arriyaz.nstu
▴ 30
2
votes
10
replies
4.4k
views
CWL: Getting the outputs(File) of a command line tool
Common-Workflow-Language
cwl
updated 15 days ago by
Ram
40k • written 6.4 years ago by
kevin.o.oluoch
▴ 70
3
votes
10
replies
501
views
STAR index not working
STAR
RNA-Seq
5 days ago by
camillab.
▴ 130
785 results • Page
1 of 16
Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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▴ 550
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Answer: Fetch Fastq files directly for SRA data
by
Rob
6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe
by
YUYANG.OON
• 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject
by
Jordan M Eizenga
▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis?
by
Chris
▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject
by
Qi
• 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject
by
Jordan M Eizenga
▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis?
by
Yogi
▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions
by
Yogi
▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question
by
Istvan Albert
98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate
by
dsull
★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian)
by
morovatunc
▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes?
by
Michael
53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate
by
Mehwish
• 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting
by
Ram
40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
bk11
★ 1.2k
I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
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