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326 results • Page 1 of 7
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0
votes
0
replies
11
views
How to create a mutation frequency comparison plot?
R data-visualization plot
50 minutes ago by saipra003 ▴ 10
0
votes
0
replies
17
views
How to find node Postion and source(sample) ?
vg
1 hour ago by zhang yi xing ▴ 20
0
votes
0
replies
20
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle protein alignment
2 hours ago by Richard Fontaine • 0
0
votes
3
replies
57
views
bwa mem hangs after a few thousand reads
bwa-mem alignment bwa calling variant
updated 38 minutes ago by 136k • written 2 hours ago by • 0
0
votes
1
reply
71
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated 3 hours ago by 12k • written 4 hours ago by ▴ 710
0
votes
2
replies
115
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq pivot_longer ggplot2
updated 4 hours ago by ★ 3.4k • written 5 hours ago by • 0
1
vote
3
replies
127
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR volcano plotting R plot
updated 3 hours ago by ★ 5.0k • written 6 hours ago by ▴ 250
0
votes
0
replies
54
views
scVelo cell transitions from marker gene expressing cells
velocity scvelo RNA
10 hours ago by rbronste ▴ 420
1
vote
3
replies
194
views
Identify clusters of populations based on gene expression
Seq Single cell RNA
updated 10 hours ago by ★ 1.5k • written 17 hours ago by ▴ 50
0
votes
1
reply
105
views
Python function to export the annotated records to genbank file using python and biopython
biopython python bioinformatic programming
updated 16 hours ago by ★ 2.0k • written 18 hours ago by • 0
1
vote
6
replies
174
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
20 minutes ago by CTLong ▴ 10
2
votes
1
reply
112
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 16 hours ago by ★ 2.0k • written 20 hours ago by ▴ 20
0
votes
0
replies
65
views
Does breadth of coverage signify expression?
Coverage breadth Bedtools Expression count
21 hours ago by Smriti ▴ 10
1
vote
4
replies
212
views
Bowtie mapping for single_end read
bowtie
11 hours ago by Rita • 0
0
votes
0
replies
64
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
22 hours ago by cook.675 ▴ 200
0
votes
0
replies
64
views
String App in Cytoscape
App String cytoscape
1 day ago by hellokwmin • 0
0
votes
0
replies
82
views
missing region in the process of annotation
annotatr minfi
1 day ago by Aki ▴ 10
1
vote
0
replies
77
views
Visualize and explore eventalign data against reference
igv minimap nanopolish nanopore ngs
1 day ago by joe ▴ 390
0
votes
4
replies
219
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq Nanopore ONT differential expression
11 hours ago by tw_140 • 0
9
votes
16
replies
668
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
6 hours ago by analyst ▴ 10
0
votes
0
replies
85
views
Differentiate sequenced and imputed variants in BGEN files
imputation bgen ukb
1 day ago by user230613 ▴ 350
0
votes
4
replies
234
views
Species coverage in the NCBI protein NR database ?
NR
updated 1 day ago by 99k • written 1 day ago by ▴ 10
0
votes
0
replies
92
views
addPatternDensity to qsea object
maxDensityPattern medip qsea
1 day ago by Jaykishan • 0
0
votes
0
replies
98
views
Harmony integration PC variance explained
scRNA integration harmony
1 day ago by e.iich • 0
0
votes
3
replies
210
views
merged rs number information
merged dbsnp
1 day ago by sskimvd • 0
1
vote
1
reply
148
views
Beginner differential methylation analysis
Methylation
updated 1 day ago by ★ 1.8k • written 2 days ago by ▴ 30
2
votes
1
reply
222
views
EnhancedVolcano underrepresenting DEGs
R
updated 15 hours ago by 86k • written 2 days ago by ▴ 30
0
votes
0
replies
102
views
[maftools]Too many multi_hit and missense mutation
maftools gatk MAF data WES VCF
2 days ago by jiazheng_lin • 0
0
votes
0
replies
114
views
Negative F statistics for sex check in plink
plink check sex
2 days ago by kl ▴ 10
0
votes
1
reply
180
views
Chipseq peak calling and peak frequency region
chipseeker macs2
updated 1 day ago by 3.2k • written 3 days ago by ▴ 10
0
votes
1
reply
234
views
issue in RNA -seq analysis
NGS RNA-Seq
updated 3 days ago by 136k • written 3 days ago by • 0
0
votes
3
replies
331
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA deconvolution Music Music2 bulk
updated 3 days ago by 78k • written 4 days ago by • 0
0
votes
0
replies
221
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
4 days ago by Wenke • 0
0
votes
3
replies
295
views
Annovar - Annotated file cells show string
annovar
4 days ago by Roshan • 0
0
votes
1
reply
230
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW MinION Nanopore
updated 4 days ago by 136k • written 4 days ago by ▴ 40
0
votes
0
replies
153
views
htShinyExample-5.3 - not working
htShiny Oncoprint InteractiveComplexHeatmap
4 days ago by bioinfo ▴ 60
0
votes
0
replies
154
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA Worms RNA-Seq
4 days ago by kdca • 0
0
votes
3
replies
266
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
4 days ago by Sara ▴ 230
0
votes
0
replies
800
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
0
votes
0
replies
149
views
not best k value found
de assemblly assembly novo kmergenie
4 days ago by shaileshdesai76 • 0
0
votes
0
replies
158
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR ribo-seq multi-mapped rna-seq TE
5 days ago by Carmen • 0
0
votes
0
replies
164
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq deseq2
5 days ago by pl23 • 0
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single ORA nucleus mRNA Homer
21 hours ago by je71xusa • 0
0
votes
2
replies
260
views
Tool to get genes in the neighbourhood of a particular gene
locus Gene
updated 5 days ago by ★ 1.3k • written 5 days ago by ▴ 80
2
votes
8
replies
578
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR Salmon mapper aligner RNAseq
updated 1 day ago by 136k • written 7 days ago by ▴ 10
5
votes
2
replies
235
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
190
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole genome assembly sequencing
updated 5 days ago by 47k • written 5 days ago by ▴ 10
1
vote
0
replies
134
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics proteomics multiomics
6 days ago by WUSCHEL ▴ 720
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R complexheatmap
updated 9 hours ago by ★ 1.2k • written 6 days ago by ▴ 10
0
votes
0
replies
106
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway mapping database
6 days ago by Ngrin • 0
326 results • Page 1 of 7
Recent Votes
Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
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Recent Replies
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
> even if tpe and tbo are trailing after adapter and quality trimming Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads by cee28 • 0
Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by DINESHR • 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by dsull ★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM? by rpolicastro 12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks by Ankit ▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by cmdcolin ★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by rpolicastro 12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file by ATpoint 78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
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