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How to find node Postion and source(sample) ?
vg
just now by zhang yi xing ▴ 20
0
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2
replies
77
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run ChIP-seq DiffBind
4 minutes ago by DINESHR • 0
0
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0
replies
4
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MUSCLE Protein Alignment of Distantly Related Proteins
muscle protein alignment
10 minutes ago by Richard Fontaine • 0
0
votes
0
replies
11
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bwa mem hangs after a few thousand reads
bwa-mem alignment bwa calling variant
55 minutes ago by cee28 • 0
0
votes
1
reply
42
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated 1 hour ago by 12k • written 2 hours ago by ▴ 710
0
votes
2
replies
82
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq pivot_longer ggplot2
updated 2 hours ago by ★ 3.4k • written 3 hours ago by • 0
1
vote
3
replies
102
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR volcano plotting R plot
updated 1 hour ago by ★ 5.0k • written 4 hours ago by ▴ 250
1
vote
5
replies
167
views
Generate Read counts from bam file
RNAseq reference_genome Deseq2 read_counts
updated 3 hours ago by 78k • written 6 hours ago by • 0
0
votes
1
reply
72
views
bam or VCF files from GSE75010
bam file or VCF
updated 6 hours ago by 78k • written 6 hours ago by • 0
0
votes
0
replies
79
views
Bcftools consensus when reference is a deletion
consensus vcf
6 hours ago by selplat21 ▴ 20
0
votes
1
reply
115
views
How should I run ssgsea analysis ?
functional TPM enrichment gsea ssgsea
updated 7 hours ago by ▴ 80 • written 16 hours ago by ★ 3.3k
0
votes
4
replies
206
views
How to deeply sequence long inserts
NGS phage read display Long
updated 6 hours ago by 19k • written 12 hours ago by • 0
0
votes
1
reply
80
views
VCF conservation into Treemix
Treemix Plink VCF
updated 7 hours ago by ▴ 80 • written 8 hours ago by ▴ 300
0
votes
2
replies
139
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq Normalization
6 hours ago by harter-ainsworth.izaak • 0
0
votes
0
replies
51
views
scVelo cell transitions from marker gene expressing cells
velocity scvelo RNA
9 hours ago by rbronste ▴ 420
0
votes
2
replies
133
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p-value combination methods
rnaseq NB-GLM p-value meta-Analysis
updated 4 hours ago by ★ 5.0k • written 11 hours ago by • 0
3
votes
2
replies
129
views
Moving AF tag to new column in a VCF file
mutect2 vcf
6 hours ago by Christian ▴ 30
1
vote
4
replies
205
views
How can I map coordinates between two strains of yeast?
coordinates yeast genome mapping fasta
updated 10 hours ago by 136k • written 23 hours ago by ▴ 10
0
votes
1
reply
107
views
The difference blastn output when using subject and db options
genome blastn mite annotation tracker
updated 14 hours ago by 136k • written 17 hours ago by ▴ 40
1
vote
3
replies
192
views
Identify clusters of populations based on gene expression
Seq Single cell RNA
updated 8 hours ago by ★ 1.5k • written 15 hours ago by ▴ 50
1
vote
3
replies
176
views
featureCounts results: low rate of 'Successfully assigned alignments'
FeatureCounts HISAT2 RNA-seq
updated 14 hours ago by 136k • written 16 hours ago by ▴ 10
0
votes
1
reply
103
views
Python function to export the annotated records to genbank file using python and biopython
biopython python bioinformatic programming
updated 14 hours ago by ★ 2.0k • written 16 hours ago by • 0
0
votes
2
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119
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Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
1 minute ago by GeneBC12 • 0
1
vote
1
reply
119
views
Mapping quality in `vg giraffe`
vg
updated 17 hours ago by ▴ 40 • written 22 hours ago by • 0
2
votes
1
reply
110
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 14 hours ago by ★ 2.0k • written 18 hours ago by ▴ 20
2
votes
4
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393
views
Protein Database
protein course database
updated 18 hours ago by ★ 2.3k • written 4 days ago by • 0
0
votes
0
replies
61
views
Does breadth of coverage signify expression?
Coverage breadth Bedtools Expression count
19 hours ago by Smriti ▴ 10
0
votes
6
replies
233
views
I made an error when using metawrap to binning
metagenome binning metawrap
19 hours ago by alice005201314 • 0
1
vote
4
replies
210
views
Bowtie mapping for single_end read
bowtie
9 hours ago by Rita • 0
0
votes
0
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62
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
20 hours ago by cook.675 ▴ 200
0
votes
4
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138
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MRI VBM issue
MRI VBM ROI Rhesus
21 hours ago by Ethan Lee • 0
5
votes
3
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192
views
SPAdes error: finished abnormally, OS return value: 21
SPAdes
updated 8 hours ago by 19k • written 1 day ago by ▴ 20
0
votes
4
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217
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq Nanopore ONT differential expression
9 hours ago by tw_140 • 0
1
vote
2
replies
210
views
Best practices for unstranded sequences in featureCounts
featurecounts overlapping unstranded
18 hours ago by Enrique • 0
9
votes
16
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662
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Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
4 hours ago by analyst ▴ 10
0
votes
3
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210
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merged rs number information
merged dbsnp
23 hours ago by sskimvd • 0
2
votes
1
reply
221
views
EnhancedVolcano underrepresenting DEGs
R
updated 13 hours ago by 86k • written 2 days ago by ▴ 30
2
votes
4
replies
338
views
Human mitochondrial reference genome
reference genome mitochondria
6 hours ago by singhankit973 • 0
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single ORA nucleus mRNA Homer
19 hours ago by je71xusa • 0
4
votes
9
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563
views
Working with NCBI downloadable Datasets
NCBI Genedata Datasets
updated 21 hours ago by ▴ 880 • written 6 days ago by • 0
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R complexheatmap
updated 7 hours ago by ★ 1.2k • written 6 days ago by ▴ 10
1
vote
6
replies
457
views
frequency plot for peaks
chip-seq chipseeker
updated 1 hour ago by ▴ 400 • written 15 days ago by ▴ 10
3
votes
5
replies
488
views
Circular genome browser
genome-browser circular-genome
updated 12 hours ago by ★ 3.4k • written 27 days ago by ▴ 20
3
votes
2
replies
627
views
CPTAC data, download, merge
CPTAC merging seq data RNA
updated 16 hours ago by ▴ 50 • written 16 months ago by ▴ 160
7
votes
11
replies
1.7k
views
Technical replicates in Microarray data
GEO Microarray
updated 21 hours ago by ▴ 20 • written 22 months ago by ▴ 10
4
votes
4
replies
1.9k
views
How to do simple pathway analysis?
rna-seq genome gene
updated 10 hours ago by • 0 • written 4.5 years ago by ▴ 110
46 results • Page 1 of 1
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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:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
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Recent Replies
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GeneBC12 • 0
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 …
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by ATpoint 78k
DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
Comment: p-value combination methods by dsull ★ 5.0k
Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by RNAseqer ▴ 250
Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by Nitin Narwade ★ 1.5k
Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
Comment: Construction of single sequence assembly out of contigs by analyst ▴ 10
Thanks colindaven!
Comment: Generate Read counts from bam file by Enrique • 0
Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
Comment: Generate Read counts from bam file by ATpoint 78k
No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
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