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22 results • Page
1 of 1
Sort: Votes
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Views
Votes
Replies
9
votes
16
replies
669
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
8 hours ago by
analyst
▴ 10
2
votes
1
reply
114
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 17 hours ago by
barslmn
★ 2.0k • written 21 hours ago by
jiyoung
▴ 20
2
votes
1
reply
222
views
EnhancedVolcano underrepresenting DEGs
R
updated 17 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
1
vote
6
replies
204
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
1 hour ago by
CTLong
▴ 10
1
vote
6
replies
476
views
frequency plot for peaks
chip-seq
chipseeker
updated 5 hours ago by
Ankit
▴ 400 • written 15 days ago by
Mehwish
▴ 10
1
vote
4
replies
215
views
Bowtie mapping for single_end read
bowtie
12 hours ago by
Rita
• 0
1
vote
3
replies
197
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 11 hours ago by
Nitin Narwade
★ 1.5k • written 19 hours ago by
Bine
▴ 50
1
vote
3
replies
134
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 4 hours ago by
dsull
★ 5.0k • written 8 hours ago by
RNAseqer
▴ 250
0
votes
0
replies
33
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
3 hours ago by
Richard Fontaine
• 0
0
votes
0
replies
41
views
How to find node Postion and source(sample) ?
vg
3 hours ago by
zhang yi xing
▴ 20
0
votes
0
replies
23
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
2 hours ago by
saipra003
▴ 10
0
votes
3
replies
87
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
updated 2 hours ago by
GenoMax
136k • written 4 hours ago by
cee28
• 0
0
votes
0
replies
11
views
Problem in installing 'magick' R package
R
installation
package
magick
1 hour ago by
applepie
• 0
0
votes
0
replies
67
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
22 hours ago by
Smriti
▴ 10
0
votes
2
replies
1.4k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 10 minutes ago by
jiyoung
▴ 20 • written 7 months ago by
Hayler Edu
▴ 30
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
22 hours ago by
je71xusa
• 0
0
votes
1
reply
107
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 17 hours ago by
barslmn
★ 2.0k • written 19 hours ago by
Saurabh
• 0
0
votes
4
replies
221
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
13 hours ago by
tw_140
• 0
0
votes
0
replies
56
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
12 hours ago by
rbronste
▴ 420
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 10 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
0
votes
2
replies
129
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 5 hours ago by
cmdcolin
★ 3.4k • written 6 hours ago by
Dylan C-C
• 0
0
votes
1
reply
80
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 4 hours ago by
rpolicastro
12k • written 5 hours ago by
O.rka
▴ 710
22 results • Page
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Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
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Comment: unicycler error : [Errno 13] Permission denied:
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Recent Replies
Comment: AttributeError: module 'collections' has no attribute 'Hashable'
by
jiyoung
▴ 20
Currently I am experiencing the same problem. Have you solved this?
Comment: Help doing differential expression analysis -experimental design and gProfiler T
by
rajabolacuan
• 0
Good Information Sir
Answer: Viral genes not showing up in combined mouse+virus alignment
by
cook.675
▴ 200
Hello I was curious to follow up and wonder if anyone knew why the viral genes are not showing up in the count matrix? I can't seem to solv…
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?
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