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72 results • Page
2 of 2
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0
votes
1
reply
101
views
Filter InterProScan output for a specific function
interproscan
annotation
updated 1 hour ago by
jv
▴ 780 • written 1 day ago by
Purger
• 0
0
votes
1
reply
98
views
Error, (in LoadSpliceMap) string to parse is too long
oma
LoadSpliceMap
omastandalone
orthology
updated 6 hours ago by
Adrian Altenhoff
★ 1.0k • written 12 hours ago by
ziqing
• 0
0
votes
1
reply
98
views
Index with unmasked or masked in HISAT2
masked
HISAT2
toplevel
unmasked
updated 5 hours ago by
GenoMax
125k • written 10 hours ago by
ibq.enriquepola
• 0
0
votes
4
replies
94
views
fastqc: Per base sequence content
illumina
metagenomic
fastqc
updated 1 hour ago by
jv
▴ 780 • written 4 hours ago by
khoojj
• 0
0
votes
0
replies
93
views
why count_matrix.csv generated by "prepDE.py3" showed unidentified IDs
Stringtie
RNA-seq
23 hours ago by
Pegasus
▴ 40
4
votes
3
replies
91
views
Is it possible to do bedtools multicov across the entire genome?
bedtools
depth
hg38
4 hours ago by
amy__
▴ 50
0
votes
0
replies
85
views
Mis-paired primers
amplicon
primers
Mis-paired
16 hours ago by
Sara
▴ 10
2
votes
0
replies
76
views
CircRNA extraction from bulk RNA seq datasets using CIRCexplorer2 with STAR alignment
alignment
CIRCexplorer2
STAR
8 hours ago by
choijamtsm
▴ 60
0
votes
0
replies
74
views
show amplicon like exon in UCSC/IGV
amplicon
17 hours ago by
Sara
▴ 10
0
votes
0
replies
70
views
Input data for LIMMA: unnormalised or vsn or other?
lima
normalisation
vns
7 hours ago by
Sebastian Hesse
▴ 320
0
votes
0
replies
59
views
question of exonerate output
protein
gff
exonerate
annotation
8 hours ago by
TN
• 0
0
votes
0
replies
54
views
A question about Bioinformatik analysis and experimental design / comparing 2 experiments
DEseq2
Batch-effect
updated 1 hour ago by
Ram
37k • written 4 hours ago by
Frederik
• 0
0
votes
1
reply
53
views
Novogene somatic results with GATK mutect2
Mutect2
Novogene
GATK
somatic
VCF
updated 2 hours ago by
GenoMax
125k • written 4 hours ago by
chrisgr
▴ 20
1
vote
1
reply
28
views
Dealing with missing (NA) values in my 450K methylation array dataset
minfi
PCA
expression
Methylation
R
10 minutes ago by
Edward E-B
• 0
0
votes
1
reply
29
views
snp Caenorhabditis elegans
snp
Caenorhabditis-elegans
updated 1 hour ago by
Ram
37k • written 1 hour ago by
haiminabox
• 0
0
votes
0
replies
23
views
Mapping IDs to systematic names (GOSim, setevidencelevel() )
GOSim
updated 1 hour ago by
Ram
37k • written 2 hours ago by
eliska.ochodkova
• 0
0
votes
1
reply
20
views
Size of two scRNA-Seq conditions
scRNA-Seq
updated 34 minutes ago by
rpolicastro
11k • written 49 minutes ago by
Chris
▴ 60
0
votes
0
replies
15
views
Mapping with bbmap.sh
bbtools
SAM
bbmap
28 minutes ago by
Hayler Edu
▴ 30
0
votes
0
replies
11
views
geom_errorbar not dodging or producing horizontal line
ggplot2
geom_errorbar
23 minutes ago by
bsp017
▴ 40
0
votes
0
replies
5
views
How to export ONE copy of unique sequence in Vsearch
blast
y
vsearch
taxono
uchime
updated 10 minutes ago by
andres.firrincieli
3.1k • written 13 minutes ago by
josc
• 0
0
votes
0
replies
2
views
Gene Coverage Profile generated by Qualimap clarification
Coverage
HPC
Nextflow
Bash
RNA-Seq
just now by
qstefano
▴ 20
0
votes
0
replies
2
views
News:
Course - Version Control for Researchers
VersionControl
GIT
Github
1 minute ago by
carlopecoraro2
★ 2.2k
72 results • Page
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Recent Votes
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
What type of database does gnomAD use?
What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
Answer: How can I convert this pairwise format to fasta?
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Recent Replies
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
Mensur Dlakic
★ 22k
I have no idea what cutoff is in this context, nor what you mean by `original` values. I don't know how you got those values for means. I …
Comment: Protein protein interactions
by
Mensur Dlakic
★ 22k
This is not a trivial calculation nor a simple sequence comparison like with BLAST, so it may take a while. Besides, there could be hundred…
Comment: snakemake Unexpected keyword bam in rule definition
by
Wayne
★ 1.6k
Any chance it is an indentation issue that isn't caused by what you aren't sharing here? See [here](https://groups.google.com/g/snakemake/c…
Comment: Size of two scRNA-Seq conditions
by
rpolicastro
11k
More important would be the cell QC stats (such as reads per cell and number of unique features detected per cell), the number of cells per…
Answer: What type of database does gnomAD use?
by
Jeremy Leipzig
21k
If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
by
Basti
★ 1.3k
You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
Comment: Virtual box
by
Ram
37k
This post does not fit the theme of this forum.
Comment: Filter InterProScan output for a specific function
by
jv
▴ 780
I imagine you can filter on things like E.C. numbers and domain names using `bash`, `awk`, `R`, or some other code.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
by
STARDUST
• 0
I will try both rMATS and SUPPA for categorising changes. For the specific exons, i'm expecting the last exons should be affected. That is …
Answer: snp Caenorhabditis elegans
by
GenoMax
125k
See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
by
jv
▴ 780
- NOISeq <https://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf> - Cuffdiff <http://cole-trapnell-lab.gi…
Comment: fastqc: Per base sequence content
by
jv
▴ 780
I think this is to be expected based a report I was able to find online <https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
Unless the kit directions tell you to remove remove the initial 10-15 bp you may as well leave them alone. Data should align would be my in…
Comment: RNA Editing data from RNA-seq
by
Genetics
• 0
Thank you so much for your kind reply and for helping a bioinformatics beginner like me. Can I use **bowtie2** tools for allignment and th…
Comment: fastqc: Per base sequence content
by
khoojj
• 0
Yes, I have proceed with analysis but I wonder if it is necessary to remove the first 10 or so bp from the reads. I have checked that NEBN…
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