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221 results • Page
1 of 5
Sort: Votes
Rank
Views
Votes
Replies
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 3 days ago by
Ram
40k • written 12.3 years ago by
Palu
▴ 250
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 6 days ago by
rohitsatyam102
▴ 750 • written 12.5 years ago by
Ketil
4.1k
36
votes
16
replies
28k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 6 days ago by
jkbonfield
★ 1.1k • written 4.6 years ago by
chparada
▴ 60
23
votes
12
replies
1.9k
views
Genes encoded on both strands of DNA?
Genes
strand
updated 4 days ago by
Ram
40k • written 17 months ago by
A_heath
▴ 140
19
votes
14
replies
859
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 5 days ago by
Jeremy Leipzig
21k • written 6 days ago by
vincenthus
▴ 70
18
votes
22
replies
8.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 3 days ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
16
votes
16
replies
1.8k
views
Species identifcation using 16s rRNA
16srRNA
fasta
updated 4 days ago by
Ram
40k • written 2.6 years ago by
A_heath
▴ 140
13
votes
10
replies
598
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 1 day ago by
ATpoint
76k • written 3 days ago by
MVJ
▴ 10
11
votes
4
replies
907
views
How to determine % similarity between genomes?
mauve
mugsy
genome-alignment
updated 4 days ago by
Ram
40k • written 2.5 years ago by
A_heath
▴ 140
10
votes
8
replies
560
views
Adding a control sample to bulk RNA-seq
RNA-seq
4 days ago by
Chris
▴ 180
9
votes
4
replies
1.2k
views
How to extend contigs from single-end reads?
contigs
contig-extension
updated 4 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
9
votes
4
replies
1.1k
views
Illumina Q score
Illumina
quality-score
updated 4 days ago by
Ram
40k • written 2.0 years ago by
A_heath
▴ 140
9
votes
12
replies
4.2k
views
converting a list of genes and interaction to a graph
gene
R
updated 5 days ago by
Amirhossein Hajianpour
▴ 40 • written 7.7 years ago by
fi1d18
★ 4.2k
9
votes
5
replies
7.0k
views
Genomic Bam To Transcriptome Bam
bam
samtools
updated 6 days ago by
Ram
40k • written 9.8 years ago by
dfernan
▴ 750
8
votes
5
replies
1.6k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 4 days ago by
Ram
40k • written 23 months ago by
A_heath
▴ 140
8
votes
10
replies
712
views
Inflated GWAS test statistic after merging multiple batches of genotype dataset imputed differently
genotype
imputation
gwas
updated 5 days ago by
LauferVA
3.7k • written 6 days ago by
Amy
▴ 20
8
votes
5
replies
376
views
Alphafold Cat
Joke
updated 6 days ago by
fishgolden
▴ 510 • written 14 days ago by
BioGrad321
• 0
8
votes
4
replies
786
views
BLASTn: extract unmatched regions only
BLASTn
updated 4 days ago by
Ram
40k • written 22 months ago by
A_heath
▴ 140
8
votes
2
replies
2.9k
views
How to edit fasta headers to keep only ID and organism?
fasta
updated 4 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
7
votes
3
replies
713
views
blastn with short sequences gives no results in the corresponding genome
primers
blastn
updated 4 days ago by
Ram
40k • written 2.7 years ago by
A_heath
▴ 140
7
votes
4
replies
1.9k
views
Structural variant breakend
structural-variant
updated 4 days ago by
Ram
40k • written 2.1 years ago by
A_heath
▴ 140
7
votes
7
replies
3.8k
views
Genes with promoter and enhancer regions as GTF
ChIP-Seq
featurecounts
gtf
promoter
genes
updated 3 days ago by
abis.1819104
• 0 • written 5.3 years ago by
hkarakurt
▴ 170
6
votes
1
reply
159
views
How to retrieve sample informations from given ID from Sequence Read Archives?
eutils
ncbi
SRA
updated 6 days ago by
Ram
40k • written 7 days ago by
DareDevil
★ 3.3k
6
votes
4
replies
750
views
How to rename file titles that contain underscores?
shell
bash
updated 4 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
6
votes
4
replies
1.2k
views
How to sort blast results by a minimum % of identical matches?
blast
updated 4 days ago by
Ram
40k • written 2.9 years ago by
A_heath
▴ 140
6
votes
8
replies
507
views
Find potential important genes from bulk-RNA seq experiment
RNA-seq
3 days ago by
Chris
▴ 180
6
votes
7
replies
1.2k
views
wc -l or wc -c which linux command is best to find total read count in fastq file?
linux
updated 6 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
5
votes
4
replies
738
views
Primer designing for full length gene amplification
gene-amplification
primer-design
offtopic
updated 6 days ago by
Ram
40k • written 16 months ago by
Fizzah
▴ 30
5
votes
4
replies
560
views
How to correct a wrong protein extraction from FASTA file?
fasta
bash
updated 4 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
5
votes
7
replies
469
views
Elusive syntax error in Snakefile
snakemake
updated 5 days ago by
Ram
40k • written 6 days ago by
Giuseppe Giovanni
▴ 30
5
votes
7
replies
412
views
Salmon index not progressing
salmon
updated 3 days ago by
Michael
53k • written 4 days ago by
camillab.
▴ 130
5
votes
6
replies
226
views
6 follow
Filter human transcription factors
transcription-factor
RNA-seq
updated 20 minutes ago by
Alex Reynolds
35k • written 16 hours ago by
Chris
▴ 180
5
votes
2
replies
244
views
kallisto normalized TPM values without bootstraps
tpm
cibersort
sleuth
kallisto
RNA-seq
3 days ago by
butterman16
▴ 20
5
votes
4
replies
249
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
13 hours ago by
Mehwish
• 0
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 6 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
4
votes
7
replies
724
views
How to subtract a number from protein IDs?
blast
updated 4 days ago by
Ram
40k • written 3.1 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 4 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
4
votes
3
replies
989
views
INSTALLING DEseq2 via conda
DEseq2
conda
RNA-seq
updated 6 days ago by
Ram
40k • written 4 months ago by
Fizzah
▴ 30
4
votes
4
replies
411
views
DESeq2 analysis using two featureCounts generated from different studies
RNA-seq
DESeq2
4 days ago by
abedkurdi10
▴ 190
4
votes
0
replies
192
views
Herald:
The Biostar Herald for Wednesday, September 20, 2023
herald
5 days ago by
Biostar
2.0k
4
votes
8
replies
552
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
1 day ago by
Edoardo
• 0
3
votes
4
replies
423
views
During alignment STAR has stopped at started alignment step
STAR
updated 6 days ago by
Ram
40k • written 6 weeks ago by
Santhi
• 0
3
votes
2
replies
274
views
Scanning for ultra-hot topics in science via pubmed, or using other tools
growth
pubmed
4 days ago by
LauferVA
3.7k
3
votes
10
replies
492
views
STAR index not working
STAR
RNA-Seq
4 days ago by
camillab.
▴ 130
3
votes
4
replies
384
views
Chromosome bias on RNA-Seq differential gene expression analysis
chromosome-bias
RNA-seq
3 days ago by
blz
▴ 30
3
votes
1
reply
1.2k
views
%% error in Rstudio
seurat
r
updated 3 days ago by
Ram
40k • written 2.1 years ago by
AbsaR
• 0
3
votes
2
replies
261
views
How to retrieve LoF and missense variants in WES data?
bcftools
variants
plink
SNPs
updated 5 days ago by
luffy
▴ 40 • written 5 days ago by
_quantum_girl_
▴ 10
3
votes
2
replies
322
views
Identifying common DEGs among multiple datasets
R
DEG
updated 4 days ago by
Barry Digby
★ 1.2k • written 5 days ago by
Shma
• 0
3
votes
2
replies
419
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 5 days ago by
yhdist
▴ 70 • written 8 days ago by
Cookin
• 0
3
votes
1
reply
188
views
What is the difference between norm --multiallelics -any versus --atomize?
bcftools
updated 5 days ago by
Ram
40k • written 5 days ago by
a615ebfb
▴ 30
221 results • Page
1 of 5
Recent Votes
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
Comment: Calculation of TMB on gene level
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: ATAC-seq troubleshoot - Just Noise
t2t human reference genome for RNA-seq
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Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
by
Alex Reynolds
35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
by
Alex Reynolds
35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file
by
barslmn
★ 1.8k
Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ?
by
barslmn
★ 1.8k
Check out the 1000 genomes project. https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★ 1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites. Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups
by
ATpoint
76k
Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
To be more clear, I have RNAi data from depmap with different cell lines and I separated them into two groups according to their EGFR mutat…
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
You have reads, so sequencing is obviously fine. This is how the banding should look: https://kb.10xgenomics.com/hc/article_attachments/360…
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
by
Basti
★ 1.7k
Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : https://www.bio…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file
by
Patrick
• 0
Thank you James for the response; My problem is only if I want to use the output of LD pruning in a different software, like STRUCTURE (to …
Answer: Average Coverage after Assembly (Spades)
by
taniapsduarte
• 0
Hi, I'm running into the same issue. Did you make it work? Or did you find an alternative method? Thanks!
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