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77 results • Page
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0
votes
0
replies
76
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
1 day ago by
Jaykishan
• 0
0
votes
0
replies
107
views
RNASeq vs TermSeq
RNAseq
statistics
TermSeq
6 days ago by
npb27
• 0
0
votes
0
replies
67
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
1 day ago by
user230613
▴ 350
0
votes
0
replies
106
views
cNMF vs LIGER
NMF
correction
batch
5 days ago by
e.r.zakiev
▴ 170
0
votes
0
replies
838
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
24
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
updated 39 minutes ago by
GenoMax
136k • written 2 hours ago by
GeneBC12
• 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
106
views
jellyfish histo is empty
jellyfish
kmer
fastq
6 days ago by
m.t.lorenc
• 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
60
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
16 hours ago by
tw_140
• 0
0
votes
0
replies
162
views
How to perform analysis with given copy number variation datasets between disease and control cohorts
CNV
analysis
6 days ago by
Tsin-Lau
• 0
0
votes
0
replies
104
views
Interpretation of mean-variance trend in voom
EdgeR
Voom
updated 6 days ago by
Ram
41k • written 7 days ago by
Ivana
• 0
1
vote
0
replies
56
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
15 hours ago by
joe
▴ 390
0
votes
0
replies
59
views
missing region in the process of annotation
annotatr
minfi
11 hours ago by
Aki
▴ 10
0
votes
0
replies
45
views
String App in Cytoscape
App
String
cytoscape
9 hours ago by
hellokwmin
• 0
0
votes
0
replies
43
views
How can I map coordinates between two strains of yeast?
coordinates
yeast
genome
mapping
fasta
9 hours ago by
Jimmy
▴ 10
0
votes
0
replies
112
views
Low mapping after Cufflinks assembly
assembly
gffread
cuffmerge
Cufflinks
RSEM
6 days ago by
sofiablancoglez
• 0
0
votes
0
replies
39
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
5 hours ago by
cook.675
▴ 200
0
votes
0
replies
39
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
4 hours ago by
Smriti
▴ 10
0
votes
0
replies
106
views
KEGG module and abundance of its KEGG Orthologs for functioning
function
kegg
abundance
6 days ago by
Jonathan Yoou
▴ 60
0
votes
0
replies
156
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
4 days ago by
Carmen
• 0
0
votes
0
replies
161
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
4 days ago by
pl23
• 0
0
votes
0
replies
147
views
not best k value found
de
assemblly
assembly
novo
kmergenie
4 days ago by
shaileshdesai76
• 0
0
votes
0
replies
756
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
4 days ago by
Mark
• 0
1
vote
0
replies
131
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
5 days ago by
WUSCHEL
▴ 720
0
votes
0
replies
153
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
3 days ago by
kdca
• 0
0
votes
0
replies
152
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
3 days ago by
bioinfo
▴ 60
77 results • Page
2 of 2
Recent Votes
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
The Biostar Herald for Monday, November 27, 2023
Comment: use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl
Answer: Best practices for unstranded sequences in featureCounts
Answer: DEseq2 input
Comment: Filter out ALT contigs from CRAM
Answer: Bowtie mapping for single_end read
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Popular Question
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Hamtaro
▴ 10
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to
Ivan
▴ 60
Student
to
Rafael Soler
★ 1.2k
Popular Question
to
luffy
▴ 110
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Tao
▴ 30
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ashaneev07
▴ 20
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cfourps
▴ 10
Recent Replies
Comment: unicycler error : [Errno 13] Permission denied:
by
barslmn
★ 2.0k
This is not really a bioinformatics question. Either you're not the owner or in the group of the directory or the directory don't have wr…
Comment: Python function to export the annotated records to genbank file using python and
by
barslmn
★ 2.0k
Could you paste the error as printed to your screen?
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
I have found dedup.sh script of bbmap tool that removes duplicated sequences. Also there is a seqtk tool. Is it safe to remove duplicated s…
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
Hamtaro
▴ 10
Thank you for your reply. I how can I identify why I have soo many multimapping reads? The samples comes from blood from patients under d…
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
Honestly I have not assessed duplication after assembly. However I used trimmomatic for data filtration before assembly. Trimmomatic param…
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
by
kvn95ss
▴ 20
I could see the following clues from - hisat2 - ```23026867 (61.37%) aligned concordantly >1 times``` And from featureCounts - ``` Mu…
Comment: CPTAC data, download, merge
by
Mohita
▴ 50
I am also facing the same problem. I will be grateful if you help me out for this.
Comment: Circular genome browser
by
giammafer
▴ 20
Thank you very much for organising the 'awesome-genome-visualization' collection. I searched in your database before I made this question …
Answer: Mapping quality in `vg giraffe`
by
Xian
▴ 30
You can find a complete definition of how giraffe finds mapq's in the supplement of the paper: https://www.science.org/doi/10.1126/science.…
Comment: Construction of single sequence assembly out of contigs
by
Michael
53k
This looks actually quite like an "improvement", if it is one. Whether you use additional methods or not, the name of the software has been…
Answer: Protein Database
by
Elisabeth Gasteiger
★ 2.3k
Please don't hesitate to contact the UniProt helpdesk (https://www.uniprot.org/contact) if you need help with any query that would allow yo…
Comment: Best practices for unstranded sequences in featureCounts
by
Enrique
• 0
Thank you so much. Well, it’s not my intention to resolve my problem only with featureCounts, but I want to know the best arguments in that…
Comment: I made an error when using metawrap to binning
by
alice005201314
• 0
Also, I checked the output file and did not find the presence of the tmp-samtools.0000.bam file, which appears to be a temporary file that …
Comment: Find Genes in Homer Analysis that have the enriched Motif
by
je71xusa
• 0
I input a list of gene names like here http://homer.ucsd.edu/homer/microarray/index.html
Comment: I made an error when using metawrap to binning
by
alice005201314
• 0
The paragraph at the end of the log file may be the problem [M::mem_pestat] skip orientation RR as there are not enough pairs [M::…
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