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326 results • Page
1 of 7
Sort: replies
Rank
Views
Votes
Replies
2
votes
20
replies
1.6k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
26 days ago by
Maxine
▴ 30
15
votes
16
replies
819
views
ncbi error report log for validate fastq issue
sra-tools
updated 6 days ago by
GenoMax
135k • written 6 days ago by
1769mkc
★ 1.1k
3
votes
15
replies
566
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
5 days ago by
ella
• 0
0
votes
13
replies
611
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
10 days ago by
Y
• 0
2
votes
13
replies
1.5k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 7 days ago by
Ram
40k • written 6 weeks ago by
epianalysis
• 0
1
vote
11
replies
796
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 9 days ago by
GenoMax
135k • written 5 weeks ago by
langziv
▴ 50
0
votes
11
replies
771
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
13 days ago by
evmae
• 0
1
vote
10
replies
928
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 10 days ago by
jeffhsu3
• 0 • written 3 months ago by
fra.silvestro99
▴ 10
3
votes
10
replies
551
views
STAR index not working
STAR
RNA-Seq
12 days ago by
camillab.
▴ 140
0
votes
10
replies
257
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
3 hours ago by
langziv
▴ 50
2
votes
10
replies
2.8k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 5 days ago by
Raygozak
★ 1.4k • written 5.2 years ago by
kakukeshi
▴ 80
2
votes
9
replies
525
views
Calculation of TMB on gene level
genomics
updated 7 days ago by
svp
▴ 590 • written 8 days ago by
smrutimayipanda
▴ 20
0
votes
9
replies
1.0k
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 7 days ago by
rfran010
▴ 840 • written 19 days ago by
pb11
▴ 10
0
votes
9
replies
241
views
Deseq2 error
R
deseq2
4 hours ago by
sgadila
• 0
0
votes
7
replies
792
views
Mugsy error -directory must be a directory
Mugsy
updated 12 days ago by
Ram
40k • written 2.8 years ago by
A_heath
▴ 140
0
votes
7
replies
2.7k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 18 days ago by
Ram
40k • written 5.3 years ago by
AP
▴ 80
2
votes
7
replies
707
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 1 day ago by
Ram
40k • written 11 days ago by
Can Abdullah
• 0
2
votes
7
replies
699
views
VG mapping paired-end reads: error [xg]: multiple hits for XXX
variation-graph
reads
pangenome
vg
paired-end
29 days ago by
nkls063408
• 0
0
votes
7
replies
956
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 7 days ago by
rfran010
▴ 840 • written 20 days ago by
ccbb7aab4
▴ 20
1
vote
7
replies
3.6k
views
Adjust width of annotations in pheatmap
R
heatmap
updated 2 days ago by
Kevin Blighe
86k • written 4.9 years ago by
divya.nandakumar
▴ 30
5
votes
7
replies
453
views
Salmon index not progressing
salmon
updated 11 days ago by
Michael
53k • written 12 days ago by
camillab.
▴ 140
1
vote
6
replies
722
views
18S sequence not matching 18S sequence in assembly
18S
BLAST
updated 1 day ago by
Ram
40k • written 3.2 years ago by
kristina.mahan
▴ 160
0
votes
6
replies
854
views
Illumina reads mapped back onto contigs have gaps
illumina
updated 1 day ago by
Ram
40k • written 3.0 years ago by
kristina.mahan
▴ 160
2
votes
6
replies
270
views
Match variants from RNAseq with known databases
dbsnp
SNP
vcf
bcftools
RNA-seq
1 day ago by
dilokef367
• 0
0
votes
6
replies
293
views
gene correlations in between two groups
gene-expression
correlation
7 days ago by
biology_inform
▴ 40
4
votes
6
replies
396
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
updated 6 days ago by
Istvan Albert
98k • written 10 days ago by
Athena
• 0
1
vote
5
replies
299
views
CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
R
Picard
CollectRnaSeqMetrics
updated 5 days ago by
Ram
40k • written 6 days ago by
camillab.
▴ 140
8
votes
5
replies
365
views
Frustrated with DEA results
microarray
differential-expression
updated 5 days ago by
dsull
★ 4.8k • written 6 days ago by
jopadrosa
• 0
1
vote
5
replies
402
views
Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
R
edgeR
limma
RNA-seq
updated 4 days ago by
LChart
3.4k • written 6 days ago by
svlachavas
▴ 780
3
votes
5
replies
415
views
Ensembl site unresponsive in clusterProfiler analyses
parallell
clusterProfiler
R
updated 26 days ago by
manaswwm
▴ 440 • written 28 days ago by
enanoide
• 0
2
votes
5
replies
389
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 7 days ago by
ATpoint
77k • written 11 days ago by
vk
▴ 40
2
votes
5
replies
479
views
Dowload data from password protected cloud storage
data-transfer
wget
rclone
updated 25 days ago by
Joe
21k • written 26 days ago by
Paula
▴ 60
4
votes
5
replies
517
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
16 days ago by
psm
▴ 100
0
votes
5
replies
490
views
Convert gene id's to gene symbol preserving gene id's in deseq2
ensembl
r
DE
deseq2
updated 17 days ago by
Ram
40k • written 19 days ago by
dylannicoembros
• 0
8
votes
5
replies
1.6k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 12 days ago by
Ram
40k • written 24 months ago by
A_heath
▴ 140
0
votes
5
replies
476
views
genome data downloads for various strains
gisaid
hass-marr
updated 8 days ago by
Ram
40k • written 12 days ago by
iftikharmaryam123
• 0
1
vote
5
replies
244
views
bcftools error merging two VCFs: REF prefixes differ
bcftools
VCF
7 days ago by
Shane
• 0
1
vote
5
replies
538
views
Idat raw data conversion
idat
updated 16 days ago by
Giulio Genovese
▴ 330 • written 17 days ago by
Zi
• 0
0
votes
5
replies
1.3k
views
What Coverage allele-fraction threshold to use?
allele-fraction
snps
updated 1 day ago by
Ram
40k • written 2.5 years ago by
kristina.mahan
▴ 160
1
vote
5
replies
969
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx
differential-expression
t-test
deconvolution
21 days ago by
Sam
▴ 290
1
vote
5
replies
309
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
7 days ago by
omer.shomrat
• 0
0
votes
5
replies
375
views
manhattan plot with vcf information
R
manhattan
vcf
updated 12 days ago by
dthorbur
▴ 560 • written 14 days ago by
sooni
▴ 10
3
votes
5
replies
1.0k
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio
purge_dups
Assembly
bionano
updated 19 days ago by
colindaven
5.5k • written 2.7 years ago by
pablo
▴ 280
1
vote
5
replies
673
views
Mugsy percentage of identity
Mugsy
Genome-alignment
updated 12 days ago by
Ram
40k • written 2.6 years ago by
A_heath
▴ 140
2
votes
5
replies
390
views
Cluster annotation in single cell
Single-cell
updated 27 days ago by
Ram
40k • written 27 days ago by
synat.keam
▴ 80
2
votes
4
replies
394
views
join the control replicates
RNA-seq
updated 18 days ago by
seidel
11k • written 19 days ago by
Jean Pierre
• 0
1
vote
4
replies
332
views
htseq-count reports count values for deleted genes
rna-seq
htseq
22 days ago by
kmyers2
▴ 80
0
votes
4
replies
642
views
CAZy database has multiple family sequence...
metagenomics
cazy
annotation
updated 27 days ago by
JyiYeung
• 0 • written 9 months ago by
GYUDAE
• 0
3
votes
4
replies
335
views
Visualization of multiple sequence alignment quality
blastp
blast
msa
updated 28 days ago by
GenoMax
135k • written 28 days ago by
dec986
▴ 370
2
votes
4
replies
3.3k
views
Converting different annotation file formats (GTF/GFF/BED) to each other
rna-seq
next-gen
updated 1 hour ago by
alejandrogzi
▴ 30 • written 6.0 years ago by
Javad
▴ 150
326 results • Page
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Answer: tensorQTL interaction issue
Answer: Script for getting summary statistic of any genome using GTF or GFF3 ?
Comment: How do you validate and verify your pipeline's software updates?
Comment: How do you validate and verify your pipeline's software updates?
Answer: GSEA with GO and KEGG datasets
GSEA with GO and KEGG datasets
Answer: Exporting DEGs obtained from DESeq2
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Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
Kevin Blighe
86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF
by
alejandrogzi
▴ 30
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other
by
alejandrogzi
▴ 30
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
Answer: How Do I Convert From Bed Format To Gff Format?
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Answer: tensorQTL interaction issue
by
Solal
• 0
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no h…
Answer: The Biostar Handbook. A bioinformatics e-book for beginners.
by
Qboy
• 0
Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Thanks. I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
avelarbio46
▴ 30
Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
> so I don't think the genome size is available. Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
Comment: Kimura% of calcDivergenceFromAlign output
by
睿紘
• 0
For additional information, "Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929. I just rem…
Comment: Understanding mother and father alleles in VCF file
by
c.
• 0
actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
Correct. Data that went into the assembly.
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