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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
135
views
OrthoFinder problem
Sub
OrthoFinder
iterative
processes
Bash
5 hours ago by
HERMAN
▴ 10
4
votes
2
replies
152
views
Forum:
advice on course selection for a bioinformatics career.
career
updated 1 day ago by
Istvan Albert
97k • written 1 day ago by
Aaron
• 0
0
votes
1
reply
118
views
Error when using compareCluster from enichment
compareCluster
updated 8 hours ago by
Basti
★ 1.4k • written 1 day ago by
jacob
• 0
0
votes
0
replies
91
views
Need Help Scraping MeSH terms from Pubmed
Python
Entrez
Scraping
updated 23 hours ago by
Ram
38k • written 1 day ago by
Arnau
• 0
1
vote
1
reply
112
views
NA14622 data for benchmarking
benchmarking
vcf
bed
GiAB
updated 1 day ago by
GenoMax
127k • written 1 day ago by
emmanouil.a
▴ 110
0
votes
2
replies
154
views
How to add gene information below the BSmooth result ?
BSmooth
methylation
DNA
18 hours ago by
diqixiaoyaoer
▴ 10
1
vote
1
reply
130
views
Plot in R: Presence of bacteria type A vs bacteria type B in different groups
boxplot
phyloseq
plot
abundance
ggplot2
R
updated 1 day ago by
Basti
★ 1.4k • written 1 day ago by
flourde
• 0
2
votes
1
reply
99
views
Fastqc lsequence duplication and per base sequence content failed
RNA-seq
fastqc
updated 1 day ago by
GenoMax
127k • written 1 day ago by
waqaskhokhar999
▴ 150
3
votes
12
replies
487
views
prefix extraction and preparation for mapping and variant calling
bash
updated 4 hours ago by
Joe
20k • written 5 days ago by
Human
• 0
3
votes
4
replies
1.3k
views
Nextflow memory issues custom config -c
nextflow
updated 1 day ago by
ATpoint
70k • written 14 months ago by
louisber2765
• 0
2
votes
3
replies
164
views
wrong quality plots in fastqc output
fastqc
quality
samtools
fastq
wgsim
21 hours ago by
poecile.pal
▴ 50
1
vote
5
replies
284
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 21 hours ago by
Trivas
▴ 680 • written 1 day ago by
TJay
• 0
7
votes
9
replies
372
views
7 follow
Snakemake vs Nextflow Upcoming bioinformatics Project
Programming
Masters
updated 3 hours ago by
colindaven
4.5k • written 1 day ago by
rackbersingh
• 0
1
vote
1
reply
123
views
Why GATK is slow with haplotypecalling
GATK
HaplotypeCalling
updated 1 day ago by
Pierre Lindenbaum
153k • written 1 day ago by
rj.rezwan
• 0
0
votes
0
replies
93
views
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
NGS
bcftools
vcf
phase
1 day ago by
zhangfish
▴ 40
0
votes
0
replies
79
views
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
1 day ago by
Joana
• 0
0
votes
0
replies
116
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
1 day ago by
firestar
★ 1.5k
0
votes
0
replies
103
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
1 day ago by
predeus
★ 1.8k
0
votes
0
replies
103
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
1 day ago by
ucbtep
▴ 20
3
votes
1
reply
250
views
TCGA Methylation Data and Gene Mapping
Methylation
Cancer
TCGA
updated 1 day ago by
Basti
★ 1.4k • written 2 days ago by
James
▴ 30
0
votes
0
replies
128
views
Dnaplotter
Artemis
1 day ago by
prs
• 0
0
votes
2
replies
518
views
Databases to check variant pathogenicity
WholeExomeSequencing
updated 1 day ago by
AtenaLia
▴ 30 • written 13 months ago by
Fatemeh Nabizadeh
▴ 10
12
votes
14
replies
4.2k
views
7 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 7 hours ago by
Damianos P. Melidis
▴ 40 • written 2.8 years ago by
Eugene A
▴ 170
2
votes
1
reply
187
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 1 day ago by
Basti
★ 1.4k • written 1 day ago by
Stefanus C.B.
• 0
0
votes
2
replies
167
views
mrbayes segmentation fault
mrbayes
segmentation
fault
1 hour ago by
dgrace999
• 0
0
votes
0
replies
120
views
Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot
TSS
GRanges
EnrichedPlot
promoters
GenomicRanges
1 day ago by
melissachuaphd
• 0
0
votes
0
replies
112
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
1 day ago by
William
▴ 10
0
votes
0
replies
139
views
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
GSVA
limma
R
1 day ago by
Tadeoye
▴ 30
1
vote
2
replies
178
views
How to adjust for multiple batches using Combat-Seq
ComBat
RNA-seq
updated 1 day ago by
Ram
38k • written 1 day ago by
sabriledesma13
• 0
0
votes
0
replies
121
views
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
isoforms
Salmon
RNA-seq
CD45
1 day ago by
eager_underdog
• 0
0
votes
5
replies
297
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq
scRNA-seq
single-cell
genomics
ngs
updated 1 day ago by
GenoMax
127k • written 1 day ago by
O.rka
▴ 650
0
votes
2
replies
192
views
Processing fastqs generated by inDrop protocol
single-cell
rna-seq
indrop
updated 1 day ago by
Ram
38k • written 1 day ago by
bobbybobbobbo
• 0
1
vote
3
replies
251
views
How to extract/find the actual names of the gene_IDs if they are not fully presented in gtf.file, and link them to the Count.matrix
featureCounts
gtf
RNA-Seq
updated 1 day ago by
GenoMax
127k • written 1 day ago by
Pegasus
▴ 80
0
votes
1
reply
171
views
Circos plot
circos
updated 1 day ago by
Fabio Marroni
★ 3.0k • written 1 day ago by
prs
• 0
0
votes
1
reply
119
views
mpileup2sync
mpileup2sync
population2
updated 1 day ago by
Ram
38k • written 1 day ago by
Hayler Edu
▴ 30
0
votes
1
reply
2.1k
views
Blog:
list of old gene name in C. elegans
c.elegans
gene
wormbase
updated 1 day ago by
geneontologyhelp
▴ 190 • written 8.2 years ago by
firoz.imtech
▴ 50
3
votes
6
replies
320
views
Pig Reference Genome
Genome
updated 1 day ago by
Joe
20k • written 1 day ago by
anasjamshed
▴ 120
0
votes
0
replies
89
views
Number of gigabases necesary for Iso-seq-PacBio
Iso-seq
RNA-Seq
Alternative-Splicing
PacBio
updated 1 day ago by
Ram
38k • written 1 day ago by
Jesús M
• 0
0
votes
4
replies
456
views
how to create interacting Hi-C peaks
chromatin
interaction
gene
Hi-C
14 hours ago by
rheab1230
▴ 140
0
votes
2
replies
163
views
GSVA scores - positive and negative values - normalization prior to running PCA
clr
normalization
GSVA
scale
1 day ago by
Bianca
▴ 20
0
votes
2
replies
145
views
Problem with blasting UNMAPPED RNA-seq paired end reads in Jaculus jaculus
RNAseq
jaculus
unmapped
reads
1 day ago by
barbarainb
• 0
0
votes
0
replies
74
views
PGx question regarding RSIDs with more than one variant associated with it
pharmacogenomics
rsid
pgx
1 day ago by
Roy
▴ 10
0
votes
2
replies
166
views
How to calculate the Z value of infernal cmscan?
cmscan
ncRNA
infernal
updated 2 days ago by
Dunois
★ 2.3k • written 2 days ago by
shelvenlone
• 0
4
votes
5
replies
270
views
samtools idxstats not removing ChrM
samtools
ChIPseq
updated 1 day ago by
benformatics
3.5k • written 2 days ago by
Jen
▴ 40
2
votes
3
replies
179
views
how to get pfam id of proteins belonging to a particular family along with sequences in that family?
pfam
protein
id
interpro
sequence
1 day ago by
max
• 0
0
votes
0
replies
97
views
Converting Abricate output (.tsv) to gff3 format
gff3
convert
tsv
Abricate
2 days ago by
ghataksnd
▴ 10
0
votes
0
replies
108
views
samtools mpileup - bases string explanation
samtools
mpileup
2 days ago by
igorm
▴ 20
0
votes
3
replies
448
views
Practical Haplotype Graph -- Pathing Error
PHG
updated 2 days ago by
lcj34
▴ 220 • written 27 days ago by
wcs98
• 0
0
votes
3
replies
224
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 1 day ago by
Ram
38k • written 2 days ago by
VANSHIKA
• 0
7
votes
7
replies
445
views
Trying to install Roary with Conda results in error message
roary
conda
8 hours ago by
tobiwan
▴ 10
1,000 results • Page
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Recent Votes
Comment: getting coding exon information from Ensembl API
C: How to install TMAP
If there is a way to link two gosling html components in two <div>s.
A: Using GATK's HaplotypeCaller or Mutect2 for somatic cancer samples with no norma
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
Comment: Where do find virulence gene information in a gff/gtf file?
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Recent Replies
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
Juke34
7.7k
Don't use `--merge_loci` in your command line this was for AGAT version <1.0.0 (and only few scripts), now this is handled via the config.y…
Comment: getting coding exon information from Ensembl API
by
Ram
38k
> Because you just answer No we don't. I think you're confusing this professional forum contributed to by volunteers with a customer suppo…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
Ram
38k
Oh, you can just use TPM to do that. Within sample comparison is a completely different (and much easier) game.
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
Sian
• 0
Unfortunately yes, there does seem to be a problem with using the older version - when I came to do more analysis yesterday, the enrichKEGG…
Comment: getting coding exon information from Ensembl API
by
Sarah
▴ 30
Because you just answer when it's a stupid question or when I ask a lot of questions. This is for asking questions not for being judged by …
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
by
Manav
• 0
Thanks, tried working with the dataset and workflow. It worked.
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
BioinfoBee
• 0
@juke34 Thanks again. I changed the config.yaml *should overlapping loci (at CDS level) be merged in a single locus Only one gene is kept,…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
Thanks, I am not doing any differential. But, Can we say that 6th transcript is relatively more abundance in our sample than other transcri…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
zrm22
▴ 30
It looks like the ImputePipelinePlugin for the minimap2 run does not use the numThreads Option but rather does the numThreadsOnMachine - 2 …
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
@rob Please, Can you or people from your group answer . As I am using one of your paper as my [reference.][1] [1]: https://f1000rese…
Comment: fastq_screen error: Failed to calculate read length
by
firestar
★ 1.5k
I created the .fasta from a BAM, so I am just going to go back to the BAM and convert that to a .fastq and see if that works. But good to k…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
Ram
38k
> I have only one condition There is no "differential" then. RNAseq is a relative measure, so comparing single-condition replicates using …
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
[Salmon][1] is giving me TPM at transcript level. So, What I understand from that TPM is normalized for sequencing depth and Transcript l…
Answer: Does it possible to know what are the adjacent genes up to 1000bp upstream and
by
Alex Reynolds
34k
You could use `bedmap` from BEDOPS. Say you have a BED file of IS/transposable elements called `elements.bed` and a BED file of genes calle…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
twrl8
• 0
Ahh thank you! I thought the xmx parameter would be passed to the downstream commands called by the plugin. Then I think I definitely need…
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