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17 results • Page
1 of 1
Sort: replies
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Views
Votes
Replies
4
votes
7
replies
423
views
RNA seq analysis
DESeq
RNA-seq
25 minutes ago by
prifa
▴ 10
0
votes
4
replies
231
views
Galaxy StringTie error
stringtie
galaxy
23 hours ago by
trkfs
• 0
1
vote
4
replies
320
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 7 hours ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
0
votes
3
replies
173
views
How to access GWAVA software of data
GWAVA
updated 20 hours ago by
GenoMax
142k • written 23 hours ago by
nonaddldy
▴ 10
0
votes
2
replies
116
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
1 hour ago by
melissa.joubert
• 0
1
vote
1
reply
112
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 15 hours ago by
Ram
43k • written 20 hours ago by
kilcdincer
▴ 10
0
votes
1
reply
127
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 14 hours ago by
GenoMax
142k • written 14 hours ago by
bioinfo
▴ 150
0
votes
1
reply
91
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
5 hours ago by
sansan_96
▴ 90
0
votes
0
replies
31
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 hours ago by
njornet
▴ 20
0
votes
0
replies
14
views
ReactomeGSA
ReactomeGSA
1 hour ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
14
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
47 minutes ago by
Alexandra
• 0
0
votes
0
replies
82
views
Is there a real ground truth for CNV data?
CNV
19 hours ago by
jennyp0706
• 0
0
votes
0
replies
71
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 20 hours ago by
GenoMax
142k • written 20 hours ago by
Bhavya
• 0
0
votes
0
replies
80
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
16 hours ago by
ramiro.barrantes
• 0
0
votes
0
replies
46
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
7 hours ago by
brunofelicianodeomena
• 0
0
votes
0
replies
50
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 6 hours ago by
GenoMax
142k • written 7 hours ago by
Dude
• 0
0
votes
0
replies
29
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmap
bbmerge
3 hours ago by
chrisk
• 0
17 results • Page
1 of 1
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
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Popular Question
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matteo.levorato
• 0
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Palgrave
▴ 110
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DBScan
▴ 300
Popular Question
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chrisk
• 0
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mbrav005
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Sofia
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jen
▴ 10
Recent Replies
Comment: RNA seq analysis
by
prifa
▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
by
dariober
14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
melissa.joubert
• 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
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