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195 results • Page
2 of 4
Sort: replies
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Views
Votes
Replies
0
votes
4
replies
250
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
3
votes
4
replies
654
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
3 days ago by
rahu
• 0
1
vote
4
replies
187
views
ScRNA data question
scRNA
Vlnplot
Samples
1 hour ago by
starswillfade
▴ 10
0
votes
4
replies
315
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 24 minutes ago by
pinheirofabiano
▴ 10 • written 3 days ago by
qudrat.nii
▴ 10
1
vote
4
replies
413
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 2 days ago by
atowns21
• 0 • written 5 months ago by
ara
• 0
3
votes
3
replies
173
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 16 hours ago by
swbarnes2
14k • written 22 hours ago by
M
• 0
2
votes
3
replies
318
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 1 hour ago by
dsull
★ 5.8k • written 16 days ago by
javanokendo
▴ 60
1
vote
3
replies
205
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
3
votes
3
replies
716
views
KissDE and batch effect
kissDE
kissplice
4 days ago by
david.b.rombaut
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
3
votes
3
replies
218
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Estevão
• 0
6
votes
3
replies
179
views
Interpretting IGV output
IGV
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
analyst
▴ 30
0
votes
3
replies
481
views
python file for coding potential calculator
cpc2.py
updated 3 days ago by
atharvakarkare14
▴ 10 • written 7 days ago by
Ashok
• 0
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 1 day ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
0
votes
3
replies
206
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 3 days ago by
mchour
• 0 • written 3 days ago by
rhossen
• 0
2
votes
3
replies
195
views
from row count to tpm
tpm
row-count
normalization
3 days ago by
michelafrancesconi9
▴ 20
1
vote
3
replies
248
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
2
votes
3
replies
285
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 3 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
emmanouil.a
▴ 120
3
votes
3
replies
191
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
c_u
▴ 520
0
votes
3
replies
366
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 3 days ago by
colindaven
6.4k • written 11 days ago by
rj.rezwan
• 0
0
votes
3
replies
233
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 2 days ago by
Istvan Albert
100k • written 2 days ago by
Dylan
• 0
3
votes
3
replies
469
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
3
votes
3
replies
218
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Mariana
▴ 10
2
votes
3
replies
195
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
analyst
▴ 30
2
votes
3
replies
946
views
Method to detect genome doubling
CNV
genome doubling
updated 4 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
0
votes
2
replies
196
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
biochugs
• 0
0
votes
2
replies
581
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 1 day ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
1
vote
2
replies
198
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
0
votes
2
replies
190
views
Result of running of p3_in.pl
primer3
updated 4 days ago by
GenoMax
141k • written 4 days ago by
nasri
• 0
0
votes
2
replies
167
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 19 hours ago by
GenoMax
141k • written 1 day ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
164
views
Highest variable features in single cell data
single-cell
updated 18 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
213
views
Annovar using R package
Annovar
gnomAD
R
18 hours ago by
DKA
▴ 40
0
votes
2
replies
192
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 16 hours ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
4
votes
2
replies
366
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 13 hours ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
3
votes
2
replies
271
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
4 days ago by
kristiewyleung
• 0
0
votes
2
replies
420
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
6 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
199
views
PCA plot
DESeq2
PCAplot
updated 5 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
2
replies
138
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
4 hours ago by
The_PyPanda
▴ 10
2
votes
2
replies
138
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 3 hours ago by
dsull
★ 5.8k • written 9 hours ago by
Aaliya
▴ 10
0
votes
2
replies
84
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 hours ago by
GenoMax
141k • written 6 hours ago by
sapuizait
▴ 10
0
votes
2
replies
175
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
3 days ago by
sainavyav22
• 0
0
votes
2
replies
259
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
2
votes
2
replies
417
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 3 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
1
vote
2
replies
233
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 18 days ago by
Netanel
• 0
7
votes
2
replies
261
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 2 days ago by
geneontologyhelp
▴ 390 • written 3 days ago by
catherine.teyssier
• 0
2
votes
2
replies
201
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 2 days ago by
analyst
▴ 30 • written 2 days ago by
lorena9132
• 0
0
votes
2
replies
212
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
2 days ago by
mropri
▴ 150
0
votes
2
replies
797
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 1 day ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
2
replies
236
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 day ago by
Ram
43k • written 2 days ago by
v.berriosfarias
▴ 140
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 1 day ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
195 results • Page
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Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis
by
The_PyPanda
▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
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