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238 results • Page
1 of 5
Sort: Views
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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 7 hours ago by
Ram
43k • written 12.7 years ago by
Panos
★ 1.8k
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 4 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 3 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
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
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 11 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
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
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
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 7 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
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
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
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
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
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
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
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 5 hours ago by
Ram
43k • written 17 months ago by
Manav
• 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
2
votes
6
replies
3.3k
views
Base Quality of a reported variant in VCF
alignment
FASTQ
VCF
next-gen
Variant-Calling
updated 2 days ago by
Ram
43k • written 9.1 years ago by
VineethVenumadhavan
▴ 50
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
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
1
vote
8
replies
3.2k
views
cutadapt error problem
next-gen
cutadapt
updated 7 hours ago by
Ram
43k • written 5.5 years ago by
amitpande74
▴ 20
0
votes
3
replies
3.0k
views
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
R
next-gen-sequencing
absolute
updated 7 hours ago by
Ram
43k • written 6.7 years ago by
namhaesly
• 0
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 3 days ago by
axol0tl
• 0 • written 6.4 years ago by
Xinwei Han
• 0
2
votes
1
reply
2.5k
views
CRAM reference registry and the GRch38 reference genome
BAM
Samtools
GRCh38
CRAM
Variant-Calling
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
1
vote
6
replies
2.4k
views
Variant calling from multiple sequencing runs for a single samples
variant-calling
updated 2 days ago by
Ram
43k • written 6.9 years ago by
harish.nucl
• 0
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq
Somatic-Mutation
Variant-Calling
updated 2 days ago by
Ram
43k • written 6.1 years ago by
Sharon
▴ 600
1
vote
3
replies
2.4k
views
How to remove variants with 3+ alleles present Plink1.9
HaplotypeCaller
GATK
Plink1.9
vcftools
updated 6 days ago by
Jingjingzhang
• 0 • written 2.1 years ago by
ramshahaya
▴ 10
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
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
2
votes
3
replies
2.1k
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
genome
next-gen
software-error
Assembly
updated 7 hours ago by
Ram
43k • written 4.0 years ago by
memy
▴ 20
1
vote
3
replies
2.0k
views
psmc bootstrapping help
bootstrap
psmc
updated 3 days ago by
xuby963
• 0 • written 3.1 years ago by
truebeliever24
▴ 50
0
votes
1
reply
1.8k
views
Speed up PHASE software for haplotype inference
multithreading
unix
haplotype
updated 5 days ago by
WANG
• 0 • written 8.2 years ago by
kshitijtayal
▴ 40
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
1
vote
1
reply
1.8k
views
Intronic Variant Filtering
variant-calling
snp
updated 2 days ago by
Ram
43k • written 6.7 years ago by
cvu
▴ 180
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
0
votes
1
reply
1.6k
views
What is the best way to perform a PCA on .vcf of closely related bacteria?
variant-calling
updated 2 days ago by
Ram
43k • written 3.0 years ago by
d.s.account
• 0
2
votes
4
replies
1.6k
views
bowtie2 maximum value of MAPQ
bowtie2
bowtie
updated 3 days ago by
axol0tl
• 0 • written 3.6 years ago by
sami
▴ 30
0
votes
1
reply
1.5k
views
Freebayes - not detecting some ALT alleles
variant-calling
freebayes
vcf
updated 2 days ago by
Ram
43k • written 3.3 years ago by
z.klinovska
• 0
1
vote
1
reply
1.4k
views
Lowercase variants reported by SomaticSniper
variant-calling
SomaticSniper
updated 2 days ago by
Ram
43k • written 6.7 years ago by
Inés Sentís
▴ 10
0
votes
1
reply
1.4k
views
Dealing with a large sample for variant calling
NGS
alignment
variant-calling
joint-calling
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
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
1
vote
3
replies
1.2k
views
esearch get taxonomy ID from a large list of accession IDs
esearch
ubuntu
updated 1 day ago by
Bertalan_Takacs
▴ 90 • written 20 months ago by
garfield320
▴ 20
4
votes
11
replies
1.2k
views
Paired layout, but one fastq file
fastq
updated 20 hours ago by
GenoMax
140k • written 12 months ago by
Andy
▴ 120
0
votes
0
replies
1.1k
views
Effect of dbSNP build differences in variant calling
GRCh38
dbSNP
variant-calling
GATK
assembly
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
2
votes
1
reply
1.1k
views
Using the ranking value to filter
discosnp
RNA-Seq
variant-calling
updated 2 days ago by
Ram
43k • written 6.0 years ago by
vguerracanedo
▴ 10
2
votes
5
replies
974
views
Why multiple SYMBOLS, Consequences... for Variant Effect Predictor (VEP)
VEP
updated 2 days ago by
barslmn
★ 2.1k • written 15 months ago by
gernophil
▴ 80
1
vote
13
replies
965
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 3 days ago by
lcj34
▴ 410 • written 9 days ago by
b.contreras.moreira
▴ 70
1
vote
1
reply
937
views
How to remove Variants where the Ref and Alt in the reference genome are switched?
WES
NGS
Variant-Calling
updated 2 days ago by
Ram
43k • written 5.7 years ago by
O.ibra
▴ 10
1
vote
2
replies
927
views
How to display gene expression after Harmony correction in scRNA-seq analysis
scRNA-seq
correction
Harmony
5 days ago by
tujuchuanli
▴ 100
1
vote
2
replies
916
views
Jupyter notebook installation
Jupyter
updated 1 day ago by
chictu
▴ 10 • written 7 months ago by
sarahmanderni
▴ 100
238 results • Page
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Recent Votes
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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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…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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