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19 results • Page
1 of 1
Sort: replies
Rank
Views
Votes
Replies
3
votes
6
replies
386
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 1 hour ago by
jv
★ 1.2k • written 1 day ago by
newbee
▴ 40
0
votes
4
replies
1.2k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata
functional-annotation
BRAKER
MAKER
updated 7 hours ago by
ben@f
• 0 • written 11 months ago by
javanokendo
▴ 20
0
votes
2
replies
251
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
23 hours ago by
junli1988
• 0
0
votes
1
reply
129
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
updated 6 hours ago by
cmdcolin
★ 3.4k • written 23 hours ago by
Trevor
• 0
0
votes
1
reply
375
views
Loftee no splice site annotations
Loftee
VEP
updated 19 hours ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
0
votes
1
reply
105
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
updated 14 hours ago by
GenoMax
136k • written 21 hours ago by
Nicolas
• 0
0
votes
1
reply
98
views
doubt about usage of megahit
trinity
megahit
updated 4 hours ago by
Istvan Albert
99k • written 10 hours ago by
meera
• 0
0
votes
0
replies
56
views
Osmotic permeability of water transport in aquaporins
permeability
Osmotic
transport
Water
11 hours ago by
Peerzada
• 0
0
votes
0
replies
85
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
19 hours ago by
Ty
• 0
0
votes
0
replies
68
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
21 hours ago by
luckyday1661
• 0
0
votes
0
replies
65
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools
softclip
5 hours ago by
ManuelDB
▴ 80
0
votes
0
replies
55
views
Significance of several BUSCO target IDs for the same gene
target_id
sequence-ontology
BUSCO
duplication
4 hours ago by
CoLa
• 0
0
votes
0
replies
10
views
Are 10x cellranger-arc ATAC bam files deduplicated?
singlecell
10x
just now by
WaterMetal
• 0
0
votes
0
replies
42
views
How to identify CG, CHG, or CHH from MeDIP data
CHG
software
CHH
CG
MeDIP
3 hours ago by
Tm
★ 1.1k
0
votes
0
replies
83
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
23 hours ago by
bioinfo
▴ 140
0
votes
0
replies
22
views
Using TCGA-LUAD RNAseq that had already corrected batch effect in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
1 hour ago by
fluke
• 0
0
votes
0
replies
5
views
Issue with genetic QC sex check
plink
31 minutes ago by
kl
▴ 10
0
votes
0
replies
78
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
18 hours ago by
O.rka
▴ 710
0
votes
0
replies
1
view
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
motifs
promoters
bioinformatics
just now by
shome
▴ 10
19 results • Page
1 of 1
Recent Votes
Comment: Merging FASTQ files with Cellranger
Finding human .vcf files online to download
Answer: Should I scale all genes in single cell Seurat?
Answer: Should I scale all genes in single cell Seurat?
Answer: Should I scale all genes in single cell Seurat?
Answer: Problematic fastq files...How can we trust them?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
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Recent Replies
Answer: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization
by
m.habib
• 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
jv
★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands?
by
Malachi Griffith
19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
Answer: How Can I move the scattered dots more closer into the center of box ?
by
Trivas
★ 1.5k
You added a position dodge on your boxplot but not on your points.
Comment: How Can I move the scattered dots more closer into the center of box ?
by
ATpoint
78k
Please understand that biostars is not a helpdesk for trivial ggplot questions. Google it and find help on previous StackExchange sites, or…
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
jucosie
• 0
Hello, I am reviewing some old scripts in which I used clumpify.sh (BBMap 38.90) with the following parameters: ./clumpify.sh in1=$d…
Comment: Problematic fastq files...How can we trust them?
by
Istvan Albert
99k
perhaps ask her about the origin of the data, how was the data postprocessed FASTQ data is a bit more resilient than other types of data a…
Answer: GO categorization
by
Istvan Albert
99k
If you have an organism that lacks the GO to gene mapping then you have to find a way to assign these terms to your genes. Basically your …
Comment: doubt about usage of megahit
by
Istvan Albert
99k
you have not mentioned what kind of resources you have, how much data you have to process and what the expected genome/transcriptome sizes …
Comment: Problematic fastq files...How can we trust them?
by
ATpoint
78k
Then tell her to bring proper data. In the lab you also don't use buffers with mold growing in it, and in bioinformatics we don't start wit…
Comment: Problematic fastq files...How can we trust them?
by
blackadder
▴ 30
Its not my data. An external researcher is visiting and she wanted from us to do some bioinformatics... The samples were not sequenced by u…
Comment: Tools or R / Python packages to perfom ML models
by
sil_bioinfo
▴ 30
Oh, I understand. Thank you so much for your help! The truth is that there is so much information, so many packages, libraries, tutorials,…
Comment: Tools or R / Python packages to perfom ML models
by
Matthias Zepper
4.2k
Just to clarify: Many ML models are trained and executed using dedicated software libraries for machine learning and artificial intellige…
Answer: Problematic fastq files...How can we trust them?
by
ATpoint
78k
> I assume that maybe all these are fixable with a script but my question is, can we trust these files? Is it worth spending time and effor…
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