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1,000 results • Page
2 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
103
views
How to obtain de pvalue of my DMRs using Bumphunter function from minfi
DMRs
6 days ago by
Irene
• 0
1
vote
4
replies
255
views
How to filter vcf file by MAF using bcftools?
bcftools
vcf
updated 6 days ago by
Ram
40k • written 6 days ago by
_quantum_girl_
▴ 10
0
votes
3
replies
223
views
What is the correct procedure to generate a consensus bacterial sequence?
consensus
samtools
illumina
fastq
4 days ago by
marongiu.luigi
▴ 690
0
votes
2
replies
197
views
Detect STRs in illumina library
repeats
annotation
STR
5 days ago by
kirillkirilenko
▴ 20
1
vote
3
replies
333
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
5 days ago by
dalibenam64
• 0
0
votes
4
replies
287
views
Sequence quality drops in the 3' end of the left sequence in paired end. What could be the cause?
sequencing
updated 6 days ago by
GenoMax
135k • written 6 days ago by
eggrandio
▴ 40
15
votes
16
replies
820
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
0
votes
3
replies
198
views
Bug of vg surject
vg
updated 7 days ago by
Jordan M Eizenga
▴ 360 • written 7 days ago by
Qi
• 0
0
votes
1
reply
162
views
GO ENRICHMENT ANALYSIS- DESEQ
GO
updated 6 days ago by
Basti
★ 1.7k • written 7 days ago by
oduduabasi.isaiah
• 0
0
votes
1
reply
148
views
DESeq2 error - converting result object into dataframe
R
DESeq2
Shiny
updated 7 days ago by
Ram
40k • written 7 days ago by
shasabhi1
• 0
0
votes
1
reply
145
views
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
haplotype
diversity
Pegas
Arlequin
HTS_data
6 days ago by
deorugz
• 0
3
votes
3
replies
2.2k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 7 days ago by
Ram
40k • written 2.0 years ago by
Anand
▴ 40
0
votes
0
replies
107
views
How to remove chimera from 16S Sanger contigs
sanger-sequencing
chimera
uchime
updated 7 days ago by
Ram
40k • written 7 days ago by
eimanpharmacist
▴ 20
1
vote
5
replies
244
views
bcftools error merging two VCFs: REF prefixes differ
bcftools
VCF
7 days ago by
Shane
• 0
0
votes
2
replies
882
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics
transcriptome
rsem
ngs
5 days ago by
kat.bi
• 0
0
votes
2
replies
215
views
how to create a loop in R
R
offtopic
updated 7 days ago by
Ram
40k • written 7 days ago by
mthm
▴ 50
0
votes
1
reply
169
views
GO analysis after DESeq2
GO
updated 8 days ago by
Ram
40k • written 8 days ago by
oduduabasi.isaiah
• 0
3
votes
2
replies
204
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation
DMR
updated 7 days ago by
Basti
★ 1.7k • written 8 days ago by
epianalysis
• 0
0
votes
1
reply
155
views
Download an example of fully-imputed VCF files ?
VCF
impute
updated 7 days ago by
barslmn
★ 1.9k • written 8 days ago by
Ben
• 0
0
votes
0
replies
127
views
How to annotate BED for tissue expression?
BED
annotation
8 days ago by
Fabio_bie88
• 0
0
votes
1
reply
1.7k
views
error when running local chlorop1.1
chlorop
updated 8 days ago by
Ram
40k • written 7.3 years ago by
gerrychang1985
▴ 40
0
votes
6
replies
294
views
gene correlations in between two groups
gene-expression
correlation
7 days ago by
biology_inform
▴ 40
0
votes
1
reply
130
views
Running Ibex on both BCR chains?
BCR
ibex
single-cell
updated 8 days ago by
Ram
40k • written 8 days ago by
actinia94
• 0
2
votes
9
replies
528
views
Calculation of TMB on gene level
genomics
updated 7 days ago by
svp
▴ 590 • written 8 days ago by
smrutimayipanda
▴ 20
0
votes
0
replies
118
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq
spike-in
DiffBind
8 days ago by
frueher
• 0
1
vote
2
replies
166
views
Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)
regress_out
Cell_cycle
Seurat
8 days ago by
alwayshope
▴ 30
0
votes
0
replies
121
views
filtering variants in a Strelka2 VCF file based on AD and AF
Filter
VCF
9 days ago by
Bogdan
★ 1.4k
2
votes
4
replies
286
views
Integrated Seurat object change name of the two conditions
R
integrated
Seurat
8 days ago by
camillab.
▴ 140
1
vote
5
replies
310
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
7 days ago by
omer.shomrat
• 0
0
votes
1
reply
215
views
Merging the filename with tsv files for master file
genomics
updated 7 days ago by
barslmn
★ 1.9k • written 10 days ago by
smrutimayipanda
▴ 20
4
votes
6
replies
396
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
updated 7 days ago by
Istvan Albert
98k • written 10 days ago by
Athena
• 0
0
votes
0
replies
159
views
My rMATS output file is not showing gene symbols and only XLOC gene ID are being shown.
rMATS
rMATS-turbo
10 days ago by
Nipan
• 0
2
votes
4
replies
317
views
Using STAR aligner to build index of hg38
hg38
STAR
alignment
RNAseq
index
9 days ago by
Grace
• 0
0
votes
0
replies
164
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
bioinformatics
TPM
RNASeqV2
cbioportal
RSEM
updated 10 days ago by
4galaxy77
2.8k • written 10 days ago by
shakyaram079
• 0
0
votes
2
replies
286
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est
clustering
10 days ago by
Mo
▴ 40
1
vote
2
replies
270
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 8 days ago by
Zhenyu Zhang
▴ 980 • written 11 days ago by
Tahsin
• 0
0
votes
0
replies
164
views
Compare peaks between clusters in sc-ATAC
Peak-Calling
Epigenome
scATAC-seq
updated 11 days ago by
Ram
40k • written 11 days ago by
Ahmed.waraky
▴ 10
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
1
vote
3
replies
249
views
Finding sequences in unannotated genomes using reference coordinates
consensus
VCF
updated 11 days ago by
Ram
40k • written 11 days ago by
Prangan
▴ 20
0
votes
1
reply
224
views
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
RNA-seq
DNA
SMARTer
updated 11 days ago by
Ram
40k • written 11 days ago by
Mat
▴ 60
0
votes
0
replies
353
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
R
GEO
GEOmetadb
updated 11 days ago by
Pierre Lindenbaum
157k • written 11 days ago by
nonaddldy
▴ 10
2
votes
5
replies
391
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 7 days ago by
ATpoint
77k • written 12 days ago by
vk
▴ 40
0
votes
0
replies
180
views
High pvalues when using clusterProfiler for seurat
clusterProfiler
12 days ago by
Ahmed
• 0
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
0
votes
0
replies
172
views
scanpy problem for empty cells
scanpy
updated 12 days ago by
Ram
40k • written 12 days ago by
Andy
▴ 90
0
votes
0
replies
176
views
Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq
nanopore
single-cell
9 days ago by
LauferVA
3.7k
0
votes
1
reply
219
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi
cli
updated 12 days ago by
Ram
40k • written 12 days ago by
O.rka
▴ 680
0
votes
5
replies
477
views
genome data downloads for various strains
gisaid
hass-marr
updated 8 days ago by
Ram
40k • written 12 days ago by
iftikharmaryam123
• 0
0
votes
0
replies
189
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
12 days ago by
juliviglino
• 0
0
votes
1
reply
215
views
Esearch, Epost, and Efetch for Large Datasets in Biopython
eutils
biopython
entrez
updated 12 days ago by
Ram
40k • written 13 days ago by
Salem
• 0
1,000 results • Page
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A: ClusterProfiler : What is GeneRatio and BgRatio?
Answer: ClusterProfiler : What is GeneRatio and BgRatio?
Prediction of Ribosomal RNA Genes Using RNAmmer Software
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?
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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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