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824 results • Page
3 of 17
Sort: Votes
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4
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Forum:
Exploring Amino Acid Patterns in Proteins Through N-gram Analysis
protein
CAFA5
19 days ago by
Anatoly A.
▴ 10
4
votes
14
replies
4.0k
views
Trouble with bedtools getfasta
bedtools
getfasta
written 2.1 years ago by
gkunz
▴ 30
4
votes
2
replies
222
views
GFF reformator
gff
updated 19 days ago by
GenoMax
140k • written 19 days ago by
HERMAN
▴ 10
4
votes
9
replies
1.4k
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
updated 22 days ago by
ATpoint
81k • written 10 months ago by
DanielEB_fisk
▴ 20
4
votes
1
reply
2.0k
views
Common reads between two fastq files
exome
sequence
Assembly
updated 13 days ago by
Ram
43k • written 5.2 years ago by
Inquisitive8995
▴ 270
4
votes
10
replies
614
views
PDB residue serial inconsistency and PDB id&UniProt ID mismatch
pdb
UniProtID
pdbID
updated 27 days ago by
Wayne
★ 1.9k • written 28 days ago by
Nafi
• 0
4
votes
5
replies
348
views
Differential express genes in imbalance groups
Limma
8 days ago by
Chris
▴ 260
4
votes
11
replies
1.2k
views
Paired layout, but one fastq file
fastq
updated 8 hours ago by
GenoMax
140k • written 12 months ago by
Andy
▴ 120
4
votes
6
replies
291
views
Protein loops
protein
Loop
13 days ago by
Curious
▴ 10
4
votes
2
replies
298
views
Before or after LD clumping for PRS calculation in GWAS
GWAS
9 days ago by
경준
▴ 20
4
votes
8
replies
468
views
i'm trying to use STAR and there is a problem...
STAR
updated 18 days ago by
GenoMax
140k • written 18 days ago by
markusz
▴ 10
4
votes
2
replies
268
views
no permission to install to directory
R
updated 20 days ago by
Ram
43k • written 21 days ago by
sooni
▴ 20
4
votes
4
replies
1.5k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
updated 17 days ago by
cmdcolin
★ 3.7k • written 14 months ago by
Arton
• 0
4
votes
9
replies
500
views
Max length reads from fastq
fastq
updated 22 days ago by
Michael
54k • written 22 days ago by
marco.barr
▴ 30
4
votes
3
replies
1.2k
views
GATK best practices for Broad-produced NGS data
NGS
GATK4
BroadInstitute
Variant-Calling
updated 1 day ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
3
votes
4
replies
425
views
Correlation for ATAC-Seq and Chip-Seq
RNA-Seq
Chip-Seq
ATAC-Seq
29 days ago by
qudrat.nii
▴ 10
3
votes
7
replies
3.4k
views
WGCNA adjust p value
statistics
WGCNA
updated 13 days ago by
Ceren
• 0 • written 2.7 years ago by
jason.taotaotan
▴ 10
3
votes
5
replies
365
views
Tutorial for analyzing WGBS data
NGS
methylseq
WGBS
16 days ago by
pt.taklifi
▴ 60
3
votes
3
replies
407
views
I can't add VAF from population for all of my variants from VCF file
genomics
vcf
gnomad
updated 15 days ago by
Ram
43k • written 17 days ago by
Samuel
▴ 20
3
votes
2
replies
240
views
Need help in using cutadapt to trim paired end fastq reads
fastq
primer
paried-end
cutadapt
updated 21 days ago by
GenoMax
140k • written 21 days ago by
George
• 0
3
votes
7
replies
514
views
How to convert raw Nanopore R9 fast5 files to fastq files ?
dorado
fast5
basecalling
nanopore
updated 26 days ago by
GenoMax
140k • written 26 days ago by
Lélé
• 0
3
votes
5
replies
749
views
Error in openning FastQC
fastqc
igv
updated 22 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
3
votes
7
replies
522
views
Blast NCBI online using R
R
NCBI
BLAST
Rstudio
1 day ago by
Begonia_pavonina
▴ 140
3
votes
3
replies
286
views
Snakemake's SyntaxError positional argument follows keyword argument
snakemake
updated 13 days ago by
dariober
14k • written 15 days ago by
ema
▴ 10
3
votes
7
replies
426
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
21 days ago by
Fadlilah
▴ 10
3
votes
7
replies
1.3k
views
7 follow
Transcription Start Site
TSS
updated 9 days ago by
Ming Tommy Tang
★ 3.9k • written 23 months ago by
Fatemeh Nabizadeh
▴ 10
3
votes
0
replies
160
views
Herald:
The Biostar Herald for Monday, March 11, 2024
herald
16 days ago by
Biostar
2.6k
3
votes
3
replies
346
views
How to analyze DEGs in scRNA-seq data?
DEG
single-cell
scRNA-seq
rna-seq
updated 23 days ago by
Ram
43k • written 23 days ago by
kayah
• 0
3
votes
8
replies
562
views
Huge decrease of BUS records using bustools
single-cell
bustools
10X
29 days ago by
julien.wollbrett
• 0
3
votes
5
replies
328
views
scRNAseq normalization
scRNA-seq
SCT
updated 9 days ago by
ATpoint
81k • written 9 days ago by
sarahmanderni
▴ 100
3
votes
4
replies
1.4k
views
sam.gz files to bam using samtools
RNA-Seq
samtools
updated 10 days ago by
robertoalbanese.bioinfo
• 0 • written 13 months ago by
tikshyadav19
• 0
3
votes
1
reply
212
views
gene alignment (microsynteny)
alignment
microsynteny
updated 29 days ago by
cmdcolin
★ 3.7k • written 29 days ago by
gubrins
▴ 290
3
votes
3
replies
807
views
Strandness of Isoseq HiFi reads?
minimap2
pacbio
isoseq
updated 13 days ago by
Shiyi
▴ 30 • written 2.0 years ago by
compuTE
▴ 140
3
votes
4
replies
278
views
Receptors with internalization capability
receptor
13 days ago by
Shicheng Guo
★ 9.4k
3
votes
3
replies
1.4k
views
Simulate 100 Reads from .fastq file | FASTQC
fastq
FASTQC
Linux
updated 13 days ago by
Ram
43k • written 3.0 years ago by
Anonymous
▴ 10
3
votes
2
replies
271
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics
Annotation
Single
Bioinformatics
Cell
26 days ago by
Daddy
▴ 20
3
votes
8
replies
6.2k
views
6 follow
Download CAZy database
genome
gene
database
cazy
updated 12 days ago by
GenoMax
140k • written 6.1 years ago by
anu014
▴ 190
3
votes
1
reply
282
views
How to use `bai_file`/`sample_id` (cardinality=10) and `bin_id` (cardinality=2875) much efficiently here?
nextflow
23 days ago by
Đặng Hải Đăng
• 0
3
votes
2
replies
256
views
FDR and Bonferroni
FDR
Bonferroni
updated 9 hours ago by
joe
▴ 470 • written 2 days ago by
song
• 0
3
votes
4
replies
562
views
Why many organisms even though they possess mitochondrial DNA (mtDNA), it is not typically represented by chromosomes labeled as "mtDNA"?
genome
mtDNA
reference-genome
sequence
21 days ago by
George X.
• 0
3
votes
2
replies
317
views
With DESeq2 "Not full rank" Error with design
DESeq2
11 days ago by
feather-W
• 0
3
votes
12
replies
4.2k
views
samtools mpileup keeps making an empty file
samtools
pileup
updated 27 days ago by
gabt
▴ 120 • written 5.2 years ago by
James Reeve
▴ 130
3
votes
1
reply
271
views
How is strandedness preserved with PCR (DNA/RNA-seq)
PCR
strandedness
sequencing
updated 26 days ago by
Carlo Yague
8.6k • written 26 days ago by
Sotiris
• 0
3
votes
4
replies
255
views
Seqkit Replace
seqkit
fasta
updated 14 days ago by
Ram
43k • written 14 days ago by
pablo
▴ 300
3
votes
5
replies
311
views
Is it necessary to sort fastq files by sequence before running variant analysis?
fastq
NGS
sort
updated 16 days ago by
GenoMax
140k • written 17 days ago by
SlowSD
• 0
3
votes
2
replies
1.1k
views
What is the meaning of miniasm -2S6 command?
oxford-nanopore
miniasm
Assembly
updated 16 days ago by
Ram
43k • written 3.1 years ago by
traditionalGuy
▴ 60
3
votes
5
replies
376
views
Losing my mind with a VCF problem
vcf
bcftools
updated 5 days ago by
Michael
54k • written 5 days ago by
a.beggs
▴ 30
3
votes
4
replies
299
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR
MAGECK
FACS
19 days ago by
Aleksandr
▴ 10
3
votes
10
replies
652
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation
GFF
5 days ago by
Lissa Cruz Saavedra
• 0
3
votes
7
replies
510
views
wANNOVAR memory error
VCF
Annovar
updated 20 days ago by
vinayjrao
▴ 250 • written 6 weeks ago by
colourful_frog
• 0
824 results • Page
3 of 17
Recent Votes
Structural variant filtering
Trouble with bedtools getfasta
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: snippy error
Answer: TSS of protein coding genes
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Recent Replies
Comment: convert cds to seurat object
by
edoardofilippi1998
• 0
Did you check the data in the assay of the cell_data_set object?
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
use the output of `samtools mpileup`
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
ATpoint
81k
It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
Comment: Interproscan taking so much time
by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Ah, sorry, I was thinking of the wrong command. You can either use `seqtk sample` or `seqkit sample`. I would recommend the former if your …
Comment: Variant calling of GBS data
by
analyst
▴ 10
It does not output warning when I skip flags for MQRankSum and ReadPosRankSum **java -jar -Xmx30G gatk.jar VariantFiltration -R reference…
Comment: Merging featureCounts output for different species
by
andrebolerbarros
• 0
Is there any list of homology you could use for this merging? Maybe this would be helpful
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
again, remove the spaces " "SOR > 10." -> " "SOR>10"
Comment: Variant calling of GBS data
by
analyst
▴ 10
It is still giving same warning java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --fi…
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
dzisis1986
▴ 70
It doesn't make sense how to change the threads and in my case it is not working! What kind of problem is that ? is it related to Amazon to…
Comment: STAR aligner options
by
theophile
• 0
I have finally found out the reason behind this behavior. As [pointed out by dsull][1], the beginning of the alignment of read1 to the rat…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Right Pierre, thanks.
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
![enter image description here][1] [1]: /media/images/710829f2-e4af-4743-a31d-822520b4
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