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237 results • Page
1 of 5
Sort: Votes
Rank
Views
Votes
Replies
362
votes
82
replies
143k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 2 days ago by
jena
▴ 290 • written 11.1 years ago by
ole.tange
★ 4.4k
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 16 hours ago by
Ram
43k • written 12.7 years ago by
Panos
★ 1.8k
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 20 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 3 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 5 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 4 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
15
votes
10
replies
7.5k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 1 day ago by
Alex Reynolds
35k • written 8.2 years ago by
int11ap1
▴ 470
15
votes
9
replies
612
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 12 hours ago by
Dave Carlson
★ 1.7k • written 16 hours ago by
Ann
★ 2.4k
12
votes
14
replies
2.4k
views
8 follow
Forum:
Recovering bam files after unknown deletion in the storage
photorec
bam
sequencing
written 4.8 years ago by
Gabriel Wajnberg
▴ 70
12
votes
7
replies
6.7k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 3 days ago by
dsull
★ 5.7k • written 2.6 years ago by
hamarillo
▴ 70
11
votes
7
replies
894
views
Shrink logFC values after edgeR
logFC
edgeR
updated 5 days ago by
Gordon Smyth
★ 6.9k • written 8 weeks ago by
arvind.1
▴ 10
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 2 days ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 16 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
8
votes
6
replies
405
views
Pangenome of plant
pangenome
plant
updated 1 day ago by
talbots
• 0 • written 2 days ago by
analyst
▴ 10
7
votes
7
replies
3.3k
views
How to perform normalization when converting ATAC bam file to bigwig file using deeptools for IGV visualization
bamCoverage
deeptools
bigwig
IGV
ATAC
updated 6 days ago by
sgv
• 0 • written 2.2 years ago by
sir.outman
▴ 40
7
votes
2
replies
202
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 2 days ago by
gconcepcion
▴ 410 • written 2 days ago by
eorr
▴ 30
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 2 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
1 day ago by
Zeng Jingyu
▴ 60
6
votes
7
replies
623
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
6 days ago by
joe
▴ 470
6
votes
13
replies
484
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
3 days ago by
Maverick
▴ 10
5
votes
2
replies
324
views
Forum:
Can questions and answers on biostars be asked only in English? Can't I use Russian for example?
language
updated 3 days ago by
Michael
54k • written 4 days ago by
avpuzanov
• 0
5
votes
8
replies
2.2k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 2 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
5
votes
15
replies
4.7k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 6 days ago by
vague-barracuda-4686
• 0 • written 4.7 years ago by
Apprentice
▴ 160
5
votes
5
replies
5.4k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 2 days ago by
Ram
43k • written 9.3 years ago by
galbarel
▴ 10
4
votes
11
replies
1.2k
views
Paired layout, but one fastq file
fastq
updated 1 day ago by
GenoMax
140k • written 12 months ago by
Andy
▴ 120
4
votes
9
replies
905
views
Error in openning FastQC
fastqc
igv
updated 10 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
4
votes
12
replies
3.4k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 2 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 1 day ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
4
votes
2
replies
3.3k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 3 days ago by
vague-barracuda-4686
• 0 • written 16 months ago by
shinyjj
▴ 50
4
votes
9
replies
670
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 3 days ago by
Simon
▴ 10 • written 7 days ago by
Maxwell
▴ 20
4
votes
3
replies
1.2k
views
GATK best practices for Broad-produced NGS data
NGS
GATK4
BroadInstitute
Variant-Calling
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
3
votes
5
replies
381
views
Losing my mind with a VCF problem
vcf
bcftools
updated 6 days ago by
Michael
54k • written 6 days ago by
a.beggs
▴ 30
3
votes
13
replies
442
views
Variant calling of GBS data
GBS
variants
BQSR
15 hours ago by
analyst
▴ 10
3
votes
5
replies
588
views
somatic variant calling without matched normal in long-reads
variants
cancer
illumina
ONT
nanopore
3 days ago by
eesiribloom
▴ 50
3
votes
7
replies
525
views
Blast NCBI online using R
R
NCBI
BLAST
Rstudio
2 days ago by
Begonia_pavonina
▴ 140
3
votes
2
replies
105
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
16 hours ago by
DYLAN NICO
• 0
3
votes
5
replies
593
views
How to filter Illumina Nirvana variant annotation?
nirvana
filtration
updated 4 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
Kauno tvirtovės
• 0
3
votes
0
replies
126
views
Herald:
The Biostar Herald for Monday, March 25, 2024
herald
3 days ago by
Biostar
2.6k
3
votes
10
replies
656
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation
GFF
6 days ago by
Lissa Cruz Saavedra
• 0
3
votes
12
replies
640
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
1 day ago by
bioinfo_enthusiast
• 0
3
votes
2
replies
292
views
FDR and Bonferroni
FDR
Bonferroni
updated 1 day ago by
joe
▴ 470 • written 3 days ago by
song
• 0
2
votes
2
replies
293
views
Seeking help with Tcga Target Gtex Expected Count Data
R
TCGA
gTEX
5 days ago by
bioinfo_enthusiast
• 0
2
votes
2
replies
229
views
singlecell annotation
scRNA-seq
annotation
2 days ago by
kayah
• 0
2
votes
5
replies
1.8k
views
alignement and Variant calling with BWA and samtools
variant-calling
samtools
BWA
updated 2 days ago by
Ram
43k • written 2.9 years ago by
simon.burgermeister
▴ 30
2
votes
3
replies
476
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome
sequence
repeatmasker
blast
updated 1 day ago by
b.contreras.moreira
▴ 70 • written 2 days ago by
Vijith
▴ 30
2
votes
4
replies
352
views
Visualizing human genomic loci
Genome
visualization
3 days ago by
James
▴ 10
2
votes
6
replies
453
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
2
votes
3
replies
242
views
Extracting information from my VCF file
VCF
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
realtreeecat
• 0
2
votes
2
replies
4.3k
views
Variant calling for sanger reads
variant-calling
sanger
alignment
variants
updated 2 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
2
votes
11
replies
804
views
RNA seq aligner?
Alignment
4 days ago by
tesfaye
• 0
237 results • Page
1 of 5
Recent Votes
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Recent Awards •
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Teacher
to
Pierre Lindenbaum
160k
Popular Question
to
brian.fristensky
▴ 460
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Ann
★ 2.4k
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104k
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Recent Replies
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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