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20 results • Page
1 of 1
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Votes
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0
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23
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated just now by
rpolicastro
12k • written 1 hour ago by
O.rka
▴ 710
0
votes
2
replies
57
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 1 hour ago by
cmdcolin
★ 3.4k • written 2 hours ago by
Dylan C-C
• 0
1
vote
3
replies
82
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated just now by
dsull
★ 5.0k • written 3 hours ago by
RNAseqer
▴ 250
0
votes
1
reply
66
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
ChIP-seq
DiffBind
updated 40 minutes ago by
GenoMax
136k • written 3 hours ago by
DINESHR
• 0
0
votes
0
replies
50
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
8 hours ago by
rbronste
▴ 420
1
vote
3
replies
190
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 7 hours ago by
Nitin Narwade
★ 1.5k • written 14 hours ago by
Bine
▴ 50
0
votes
1
reply
102
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 13 hours ago by
barslmn
★ 2.0k • written 15 hours ago by
Saurabh
• 0
0
votes
1
reply
116
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
updated 13 hours ago by
GenoMax
136k • written 15 hours ago by
GeneBC12
• 0
2
votes
1
reply
108
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 13 hours ago by
barslmn
★ 2.0k • written 17 hours ago by
jiyoung
▴ 20
0
votes
0
replies
59
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
18 hours ago by
Smriti
▴ 10
1
vote
4
replies
207
views
Bowtie mapping for single_end read
bowtie
8 hours ago by
Rita
• 0
0
votes
0
replies
61
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
19 hours ago by
cook.675
▴ 200
0
votes
0
replies
61
views
String App in Cytoscape
App
String
cytoscape
23 hours ago by
hellokwmin
• 0
0
votes
4
replies
215
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
8 hours ago by
tw_140
• 0
9
votes
16
replies
653
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
3 hours ago by
analyst
▴ 10
0
votes
3
replies
210
views
merged rs number information
merged
dbsnp
21 hours ago by
sskimvd
• 0
2
votes
1
reply
221
views
EnhancedVolcano underrepresenting DEGs
R
updated 12 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
18 hours ago by
je71xusa
• 0
0
votes
3
replies
278
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 6 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
1
vote
6
replies
455
views
frequency plot for peaks
chip-seq
chipseeker
updated 46 minutes ago by
Ankit
▴ 400 • written 15 days ago by
Mehwish
▴ 10
20 results • Page
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Recent Votes
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?
Extract UMIs using UMI-tools
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Recent Awards •
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Popular Question
to
O.rka
▴ 710
Popular Question
to
Daniel
▴ 30
Popular Question
to
prasundutta87
▴ 660
Popular Question
to
RNAseqer
▴ 250
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Devon Ryan
104k
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Pierre Lindenbaum
158k
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Trivas
★ 1.5k
Recent Replies
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.
Answer: Generate Read counts from bam file
by
Enrique
• 0
Hello, I recommend you using the mitochondrial reference genome. For the GTF file (or GFF, they are in general the same), checkout this pos…
Comment: How to deeply sequence long inserts
by
Brian Bushnell
19k
Merging paired reads is a good idea. Then you get nice, long reads... and actually, as long as you have enough coverage, you can just mer…
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