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702 results • Page
1 of 15
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Views
Votes
Replies
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
28 days ago by
Kevin Blighe
88k
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 23 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
39
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 22 days ago by
i.sudbery
19k • written 25 days ago by
noodle
▴ 590
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 5 days ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
29
votes
28
replies
35k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 20 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 29 days ago by
Ram
44k • written 14.7 years ago by
Istvan Albert
100k
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 26 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
19
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 590
19
votes
15
replies
2.3k
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 1 day ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 19 days ago by
rsieber
▴ 10 • written 3.2 years ago by
Kumar
▴ 120
14
votes
2
replies
7.1k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 28 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
13
votes
14
replies
1.0k
views
High Malat-1 expression in single cell data
single-cell
updated 14 days ago by
t.montserrat.ayuso
▴ 40 • written 23 days ago by
carolofharvest
▴ 40
13
votes
18
replies
6.2k
views
9 follow
Blastn, need help to increase speed
RNA-Seq
blastn
blast+
updated 18 hours ago by
Dunois
★ 2.5k • written 3.2 years ago by
chiachoong_leong93
▴ 20
11
votes
3
replies
377
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 14 days ago by
b.contreras.moreira
▴ 200 • written 15 days ago by
ijarne
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 15 days ago by
Pierre Lindenbaum
162k • written 5.8 years ago by
mostafarafiepour
▴ 180
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 26 days ago by
Antonio R. Franco
★ 5.1k • written 6.1 years ago by
williamsbrian5064
▴ 520
10
votes
14
replies
842
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 15 days ago by
GenoMax
142k • written 21 days ago by
nicole.kavanagh
• 0
9
votes
23
replies
9.9k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
11 days ago by
vytarasov
▴ 180
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 12 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 11 days ago by
Ruqaiya
• 0 • written 5.8 years ago by
xiaozhongzhiping
▴ 20
8
votes
5
replies
6.7k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
8
votes
8
replies
797
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 27 days ago by
swbarnes2
14k • written 28 days ago by
Aaliya
▴ 10
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 26 days ago by
bk11
★ 2.5k • written 11 weeks ago by
Sofia
• 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 2 days ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
7
votes
2
replies
342
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 29 days ago by
geneontologyhelp
▴ 410 • written 4 weeks ago by
catherine.teyssier
• 0
7
votes
16
replies
996
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
23 days ago by
Ruqaiya
• 0
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 27 days ago by
rohitsatyam102
▴ 870 • written 6.2 years ago by
smallfish
▴ 10
7
votes
1
reply
225
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 15 days ago by
dariober
14k • written 15 days ago by
nhaus
▴ 360
6
votes
2
replies
264
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 12 days ago by
Gordon Smyth
★ 7.2k • written 13 days ago by
gBioStar5
▴ 10
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 11 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 10 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
6
votes
4
replies
383
views
Details on salmon index
Salmon
updated 5 days ago by
Rob
6.6k • written 6 days ago by
Lorenzo
• 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 17 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
6
votes
4
replies
461
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
20 days ago by
Estevão
▴ 10
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
7 days ago by
Arton
▴ 10
6
votes
7
replies
426
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
10 days ago by
sansan_96
▴ 90
5
votes
7
replies
550
views
RNA seq analysis
DESeq
RNA-seq
7 days ago by
Jacek
▴ 20
5
votes
5
replies
375
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 20 days ago by
atharvakarkare14
▴ 40 • written 20 days ago by
Begonia_pavonina
▴ 150
5
votes
5
replies
361
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
15 days ago by
Chris
▴ 280
5
votes
2
replies
456
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 27 days ago by
shalespringer
▴ 10 • written 3 months ago by
Phenylananin
▴ 20
5
votes
6
replies
643
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 22 days ago by
me
▴ 760 • written 23 days ago by
Mariana
▴ 40
5
votes
3
replies
348
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 22 days ago by
Lluís R.
★ 1.2k • written 22 days ago by
이민경[학생](대학원 융합의과학과)
• 0
5
votes
4
replies
745
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
28 days ago by
kirillkirilenko
▴ 40
5
votes
2
replies
358
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 23 days ago by
i.sudbery
19k • written 26 days ago by
vanbelj
▴ 40
5
votes
5
replies
692
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 19 days ago by
Mbofire
• 0 • written 28 days ago by
Ming Tommy Tang
★ 3.9k
5
votes
3
replies
153
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 12 hours ago by
GenoMax
142k • written 12 hours ago by
Christopher
▴ 10
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 14 days ago by
chenl
▴ 10 • written 2.6 years ago by
Martyna
• 0
4
votes
2
replies
292
views
GRCh38.gmap file
gnomix
gmap
18 days ago by
lorena9132
▴ 10
4
votes
1
reply
220
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
8 days ago by
J.
▴ 40
4
votes
0
replies
169
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
23 days ago by
Biostar
2.8k
702 results • Page
1 of 15
Recent Votes
Error when looping over multiple columns in a data frame in R
Answer: Microbial community analysis pipelines in metagenomics
A: What are chimeric reads?
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
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Comment: samtools write-index
by
LucisTheFather
• 0
``` -o alignment.sorted.bam##idx##alignment.sorted.bam.bai ``` This portion is to get .bai index, instead of .csi indexing. Although Idk th…
Comment: samtools write-index
by
LucisTheFather
• 0
Really appreciate your help Pierre! I am a little bit confused btw. do you mean this: ``` rm -vf alignment.sorted.bam.bai minimap2 -ax map-…
Comment: samtools write-index
by
LucisTheFather
• 0
Yeah, I did multiple split tests of my pipeline (just subset 400k rows of my fastq and run through my pipeline for quick tests) and none of…
Comment: Which 1000 genomes 30x files should I use for imputation?
by
David-walson
• 0
Hi there. Have you found any suggestions? I have alos been working on the 1KGP high coverage data, but i have no idea about how to use it p…
Comment: MAUVE: No gene annotations in Genbank file alignments
by
pramach1
▴ 40
The same problem persists for me too. Running progressiveMauve on command line on bunch of gbk files. Mauve itself runs fine and I do see t…
Answer: Error when looping over multiple columns in a data frame in R
by
Jeremy
▴ 910
First of all, you should use "tag.healthy" and "methods" instead of "tag.health" and "method". Also, optimal.cutpoints() wants X to be eit…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
bk11
★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files
by
a.penatauber
• 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq
by
ATpoint
82k
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP
by
Pierre Lindenbaum
162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
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