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75 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
3
votes
16
replies
578
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
updated 3 hours ago by
Michael
53k • written 1 day ago by
analyst
▴ 10
2
votes
8
replies
575
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
updated 1 day ago by
GenoMax
136k • written 7 days ago by
ian.will
▴ 10
2
votes
6
replies
2.1k
views
No best K value found
Assembly
Kmergenie
updated 4 days ago by
shaileshdesai76
• 0 • written 6.8 years ago by
kspata
▴ 80
0
votes
6
replies
486
views
Problem aligning target capture sequencing of a few hundred regions to the human reference genome
GATK4
bwa-mem
target-capture-sequencing
alignment
5 days ago by
Miguel
• 0
1
vote
5
replies
438
views
frequency plot for peaks
chip-seq
chipseeker
1 day ago by
Mehwish
▴ 10
1
vote
4
replies
284
views
Analyze with Geo2R
R
NCBI
4 days ago by
anasjamshed
▴ 120
1
vote
4
replies
127
views
Bowtie mapping for single_end read
bowtie
13 minutes ago by
Rita
• 0
0
votes
4
replies
217
views
Species coverage in the NCBI protein NR database ?
NR
updated 23 hours ago by
Istvan Albert
99k • written 1 day ago by
HERMAN
▴ 10
1
vote
4
replies
265
views
Deseq2 5 level condition - building contrast
rna-seq
deseq2
updated 6 days ago by
ATpoint
78k • written 7 days ago by
annaA
▴ 10
0
votes
4
replies
158
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
31 minutes ago by
tw_140
• 0
0
votes
3
replies
263
views
Jellyfish problem with Failed to open input file 'reads.jf'
jellyfish
kmer
fastq
6 days ago by
m.t.lorenc
• 0
0
votes
3
replies
261
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
4 days ago by
Sara
▴ 230
0
votes
3
replies
294
views
Annovar - Annotated file cells show string
annovar
4 days ago by
Roshan
• 0
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 6 days ago by
ayaosama2111
▴ 10 • written 7.0 years ago by
Nicolas Rosewick
10k
0
votes
3
replies
329
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 3 days ago by
ATpoint
78k • written 3 days ago by
manuelmourato25
• 0
0
votes
3
replies
202
views
merged rs number information
merged
dbsnp
13 hours ago by
sskimvd
• 0
0
votes
3
replies
321
views
ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
genomics
wgs
vcf
annovar
updated 6 days ago by
MatthewP
★ 1.3k • written 7 days ago by
skinny_genes
• 0
0
votes
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C
HiChIP
HiC-Pro
updated 1 day ago by
Cibo
• 0 • written 2.0 years ago by
Amina
• 0
0
votes
2
replies
269
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
9 hours ago by
je71xusa
• 0
0
votes
2
replies
255
views
Tool to get genes in the neighbourhood of a particular gene
locus
Gene
updated 5 days ago by
Raony Guimarães
★ 1.3k • written 5 days ago by
ThePlaintiff
▴ 80
2
votes
2
replies
562
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment
scDblFinder
SMART-Seq
updated 1 day ago by
e.r.zakiev
▴ 170 • written 5 months ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
253
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation
Variant
proteomics
FASTA
VCF
5 days ago by
chscho
• 0
1
vote
2
replies
280
views
Wrong in Deeptools : the enrichment of TSS and TES region are similar when using scale-region
plotprofile
computematrix
Deeptools
scale-region
5 days ago by
hao
• 0
1
vote
2
replies
190
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 5 days ago by
WouterDeCoster
47k • written 5 days ago by
manaswiniparija3
▴ 10
0
votes
2
replies
216
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
3 hours ago by
TC_Chang
▴ 10
0
votes
2
replies
193
views
how to use pilon
genome
pipelines
assembly
pilon
contig
updated 20 hours ago by
Arup Ghosh
3.2k • written 6 days ago by
vasudhapai
• 0
1
vote
2
replies
120
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 2 hours ago by
dthorbur
▴ 840 • written 6 hours ago by
Bine
▴ 50
5
votes
2
replies
234
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
4 days ago by
Rafael Soler
★ 1.2k
1
vote
2
replies
193
views
How to identify the nearest gene associated with a specific SNPs?
RSID
GWAS
updated 6 days ago by
Jeremy
▴ 840 • written 6 days ago by
camillab.
▴ 150
3
votes
2
replies
231
views
t-test by row
R
t-test
updated 6 days ago by
dthorbur
▴ 840 • written 6 days ago by
sooni
▴ 10
0
votes
1
reply
90
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 5 hours ago by
barslmn
★ 2.0k • written 8 hours ago by
jiyoung
▴ 20
1
vote
1
reply
146
views
Beginner differential methylation analysis
Methylation
updated 1 day ago by
Basti
★ 1.8k • written 1 day ago by
a.basitkhan1990
▴ 30
0
votes
1
reply
179
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 20 hours ago by
Arup Ghosh
3.2k • written 2 days ago by
Mehwish
▴ 10
1
vote
1
reply
223
views
Eigen_phred_coding values interpretation
variation
SNP
annotation
6 days ago by
Lukas
▴ 40
0
votes
1
reply
89
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 5 hours ago by
barslmn
★ 2.0k • written 7 hours ago by
Saurabh
• 0
1
vote
1
reply
513
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 1 day ago by
tingting
▴ 10 • written 7 months ago by
Chris
▴ 230
0
votes
1
reply
100
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
updated 4 hours ago by
GenoMax
136k • written 7 hours ago by
GeneBC12
• 0
2
votes
1
reply
217
views
EnhancedVolcano underrepresenting DEGs
R
updated 4 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
1
vote
1
reply
837
views
cellphonedb results visualization
cellphonedb
ktplotspy
cpdb
visulization
updated 6 days ago by
miguellarrazlopezdenovales
▴ 20 • written 10 months ago by
piotto
▴ 20
0
votes
1
reply
161
views
WGCNA convenience function
WGCNA
updated 6 days ago by
andres.firrincieli
3.5k • written 7 days ago by
fluentin44
• 0
0
votes
1
reply
228
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 3 days ago by
GenoMax
136k • written 4 days ago by
Soumajit
▴ 40
0
votes
1
reply
231
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 3 days ago by
GenoMax
136k • written 3 days ago by
subhiksha
• 0
0
votes
1
reply
132
views
error in plink
polygenicriskscore
prscalculation
prs
plink
error
updated 6 days ago by
biofalconch
★ 1.1k • written 6 days ago by
Emilija
• 0
0
votes
0
replies
82
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
1 day ago by
Jaykishan
• 0
0
votes
0
replies
117
views
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
giraffe
surject
vg
6 days ago by
cassiwatt
• 0
0
votes
0
replies
106
views
jellyfish histo is empty
jellyfish
kmer
fastq
6 days ago by
m.t.lorenc
• 0
0
votes
0
replies
122
views
Creating heatmap for ChIP-seq using deeptools
heatmap
chipseq
chip
deeptools
visualization
6 days ago by
biology_inform
▴ 50
0
votes
0
replies
851
views
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library pr…
library-prep
sequencing
ont
nanopore
ngs
6 days ago by
Mark
• 0
0
votes
0
replies
106
views
cNMF vs LIGER
NMF
correction
batch
6 days ago by
e.r.zakiev
▴ 170
0
votes
0
replies
113
views
Trouble making a ggmsa alignment plot
R
ggmsa
6 days ago by
andre.arrudalima
▴ 30
75 results • Page
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Recent Votes
Answer: Running STAR on fastq file generated from a RNA-seq experiment
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
Answer: Mapping quality in `vg giraffe`
Comment: Identify clusters of populations based on gene expression
Answer: How can I map coordinates between two strains of yeast?
Comment: Construction of single sequence assembly out of contigs
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
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Recent Replies
Comment: Bowtie mapping for single_end read
by
Rita
• 0
Thank you, ATpoint!
Comment: Bowtie mapping for single_end read
by
Rita
• 0
Thank you, Tao. We prefer bowtie to bowtie2 in this case.
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you for the suggestions! I checked some housekeeping genes and they are represented in the dataset for all samples (albeit, some at …
Answer: Moving AF tag to new column in a VCF file
by
Pierre Lindenbaum
158k
extract the vcf as a tab delimited file, something like (not tested) bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%FORMAT/AF]\n' in…
Comment: How can I map coordinates between two strains of yeast?
by
GenoMax
136k
> genome sequences of two different strains of yeast Are they the same species?
Comment: How to do simple pathway analysis?
by
he1k
• 0
Hi [AK][1], I downloaded the KO.keg file. I was wondering what tool(s) you used to generate the "KO.tsv" file as you showed here. Thanks. …
Comment: How can I map coordinates between two strains of yeast?
by
dthorbur
▴ 840
I think that is an alternative to a synteny analysis, but I only know liftover in terms of annotations. OP asks for "coordinates between th…
Comment: Bowtie mapping for single_end read
by
ATpoint
78k
I am sceptical any tweaking of parameters will make a notable difference. Parameters in bowtie are very good at default, and given it's ChI…
Comment: How can I map coordinates between two strains of yeast?
by
cmdcolin
★ 3.4k
would something like liftover not be recommended? honest question
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
▴ 840
That's good. But I still suspect this data might be really difficult to analyse. I have a handful of suggestions I would do to assess wheth…
Comment: Identify clusters of populations based on gene expression
by
dthorbur
▴ 840
One gene might not be enough data to "cluster" based on expression. Unless I'm missing something, that would just be breaking a single cont…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Yes, I performed ribosome depletion using an RNAse H based method.
Comment: Circular genome browser
by
cmdcolin
★ 3.4k
that's great to hear. one "proxy" for interactive is looking at the JS based tools, many are web based and interactive as a result. I have …
Comment: R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
by
TC_Chang
▴ 10
Hi jv, Thank you for your reply. Basically, I'm trying to generate the figure shown below with two different y-axis scales. Any suggestio…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
▴ 840
I don't have a suggestion for low yield DE analyses, but I am curious about the samples. Did you conduct any ribo-depletion steps prior to …
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