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81 results • Page
2 of 2
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0
votes
1
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71
views
Kimura% of calcDivergenceFromAlign output
repeatlandscape
repeatmasker
5 hours ago by
睿紘
• 0
0
votes
0
replies
37
views
ATAC-Seq and RPKM
RPKM
ATAC-Seq
and
4 hours ago by
qudrat.nii
• 0
0
votes
10
replies
275
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
4 hours ago by
langziv
▴ 50
0
votes
1
reply
418
views
FASTQ files for 30x 1KGP of Phase 3 data
phase3
fast
1kgp
4 hours ago by
Qboy
• 0
0
votes
0
replies
35
views
STAR Genome index Error
STAR
GenomeSAindex
4 hours ago by
Prasanna
• 0
0
votes
1
reply
453
views
Low percentage of 'Fraction Antibody Reads Usable' in Feature Barcode Cell Ranger output
scCITE-seq
feature-barcode
10x
scRNA-seq
updated 7 hours ago by
Ram
40k • written 5 months ago by
rocio.castellanos
• 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
3
replies
726
views
to annotate BEDPE files
bedtools
annotate
updated 6 days ago by
Lhl
▴ 760 • written 2.6 years ago by
Bogdan
★ 1.4k
0
votes
1
reply
144
views
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
haplotype
diversity
Pegas
Arlequin
HTS_data
6 days ago by
deorugz
• 0
0
votes
4
replies
286
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
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
0
votes
0
replies
120
views
Select minimum set of SNPs from VCF file to identify a individual
selection
SNP
6 days ago by
Bioxbio
• 0
0
votes
2
replies
197
views
Detect STRs in illumina library
repeats
annotation
STR
5 days ago by
kirillkirilenko
▴ 20
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
0
replies
137
views
Software for chimera detection of amplicon (e.g. 16S) nanopore reads
chimera
nanopore
amplicon
5 days ago by
rob_DNA
▴ 10
0
votes
0
replies
140
views
Guide for ICD-10 to EFO conversion?
icd10
efo
5 days ago by
optimistsso4co3
▴ 100
0
votes
0
replies
158
views
Convert from limma voom normalized matrix each gene to high/low
limma-voom
RNA-SEQ
updated 5 days ago by
Ram
40k • written 5 days ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
150
views
Is the concept of a cofactor in an arcsinh transformation specific to Flow Cytometry?
FlowCytometry
flowCore
FlowVS
5 days ago by
gmiller
• 0
0
votes
0
replies
151
views
Can optimal cofactors for arcsinh transformation be calculated in parallel?
parallel
R
flowcytometry
flowCore
flowVS
5 days ago by
gmiller
• 0
0
votes
1
reply
198
views
Issue with merging in plink and eigensoft.
Eigensoft
Eigenstrat
Plink
updated 5 days ago by
bk11
★ 1.4k • written 5 days ago by
Jd
• 0
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
1
reply
203
views
Unable to install HorvathMammalMethylChip40manifest packages
r
programming
updated 3 days ago by
ATpoint
77k • written 3 days ago by
Nibedita
• 0
0
votes
0
replies
128
views
In silico testing of mouse cell line expression
mouse
gene
expression
2 days ago by
Hashirama
▴ 20
0
votes
0
replies
128
views
tidy_vcf function
tidy_vcf
manhattan
vcf
updated 2 days ago by
Pierre Lindenbaum
157k • written 2 days ago by
sooni
▴ 10
0
votes
2
replies
246
views
Quality Control of VCFs that used different genotyping arrays
bcftools
VCF
1 day ago by
Shane
• 0
0
votes
0
replies
104
views
Problems encountered during the survival analysis with TCGA data
R
survival-analysis
TCGA
updated 1 day ago by
Ram
40k • written 1 day ago by
applepie
• 0
0
votes
0
replies
107
views
Problem with RNAseq MarkDuplicates(Picard)
MarkDuplicates
GATK
SNP
RNA-seq
updated 1 day ago by
Ram
40k • written 1 day ago by
Grace
• 0
0
votes
0
replies
314
views
Can plantiSMASH be used with a transcriptome instead of a genome?
plantiSMASH
updated 1 day ago by
Ram
40k • written 22 months ago by
kristina.mahan
▴ 160
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
0
votes
1
reply
1.3k
views
Convert .sqn file to .gbk
organelle
updated 1 day ago by
Ram
40k • written 2.6 years ago by
kristina.mahan
▴ 160
0
votes
0
replies
518
views
Need to fix .sqn genome annotation file prior to uploading to NCBI
sqn
NCBI
updated 1 day ago by
Ram
40k • written 2.7 years ago by
kristina.mahan
▴ 160
81 results • Page
2 of 2
Recent Votes
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?
Answer: GSEA with GO and KEGG datasets
GSEA with GO and KEGG datasets
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Popular Question
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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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