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510 results • Page
2 of 11
Sort: replies
Rank
Views
Votes
Replies
2
votes
5
replies
381
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
11 hours ago by
DanielEB_fisk
• 0
0
votes
5
replies
595
views
Making disjoint chromosomal sites contiguous with awk
awk
assembly
bash
sequence
updated 11 days ago by
Ram
39k • written 2.6 years ago by
selplat21
▴ 20
3
votes
5
replies
342
views
Uniprot API access to download .pdb files
PDB
API
Python
Uniprot
6 days ago by
jdrohan
• 0
2
votes
5
replies
438
views
How to check a gene in an open chromatin region or not?
ATAC-seq
21 days ago by
Chris
▴ 100
0
votes
5
replies
389
views
combine/merge closet variants into one from mutect2
variants
mutect2
merge
gatk
updated 15 days ago by
Istvan Albert
98k • written 20 days ago by
J.F.Jiang
▴ 900
2
votes
5
replies
379
views
RNA SEQ reads assembly for illumina sequenced data
NGS
linux
nanopore
updated 20 days ago by
Ram
39k • written 29 days ago by
Adyasha
• 0
0
votes
5
replies
453
views
Splitting heatmap
R
updated 22 days ago by
Papyrus
★ 2.5k • written 24 days ago by
hafiz.talhamalik
▴ 350
0
votes
5
replies
375
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 5 hours ago by
Zhenyu Zhang
▴ 800 • written 3 days ago by
Camilo Andres
▴ 30
0
votes
5
replies
1.4k
views
terminal can't activate base automatically (conda)
conda
updated 19 days ago by
Ram
39k • written 21 months ago by
Binghong
▴ 20
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 6 hours ago by
Ram
39k • written 5.2 years ago by
fi1d18
★ 4.2k
0
votes
5
replies
2.0k
views
error during installationi of KisSplice
cpp
c
RNA-Seq
kissplice
SNP
updated 8 days ago by
Ram
39k • written 6.8 years ago by
yoyofangliu
• 0
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna
cuffdiff
updated 6 days ago by
Ram
39k • written 4.7 years ago by
sbb
▴ 10
1
vote
5
replies
507
views
kraken on nt library
kraken
nt
7 days ago by
Francois Piumi
▴ 30
0
votes
5
replies
3.1k
views
Phylogeny Heatmap with Python
multiple-sequence-alignment
updated 14 days ago by
Ram
39k • written 4.2 years ago by
marina.gerges
• 0
5
votes
5
replies
1.6k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 12 days ago by
Ram
39k • written 5.4 years ago by
wizofe
• 0
0
votes
5
replies
841
views
trimmomatic unknown trimmer
Trimmomatic
updated 15 days ago by
Ram
39k • written 20 months ago by
Xiaoyun
▴ 10
0
votes
5
replies
1.4k
views
Best Blast Hits from Tabular Outputs in Multiple files
python
shell
blast
updated 13 days ago by
Ram
39k • written 5.6 years ago by
trini1god
• 0
0
votes
5
replies
697
views
vcftools --weir-fst-pop returns -nan
fst
vcftools
updated 13 hours ago by
mingxi
• 0 • written 5 months ago by
elizabeth
• 0
0
votes
5
replies
945
views
Bioinformatics conference with possible publication
conference
updated 5 days ago by
Ram
39k • written 4.7 years ago by
bharata1803
▴ 550
0
votes
5
replies
804
views
Read DNA sequence from FASTA rising a subclass?
FASTA
python
updated 11 days ago by
Ram
39k • written 2.6 years ago by
Gonçalo
• 0
1
vote
5
replies
3.6k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 6 hours ago by
Ram
39k • written 6.7 years ago by
Biogeek
▴ 470
3
votes
5
replies
424
views
STAR error with a loop
STAR
RNA
transcriptomics
updated 19 days ago by
Ram
39k • written 5 months ago by
luzglongoria
▴ 40
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 15 days ago by
Ram
39k • written 5.9 years ago by
CY
▴ 710
0
votes
5
replies
323
views
Problem with GPU guppy_basecaller and SLURM
nanopore
guppy
updated 7 days ago by
Medhat
9.6k • written 7 days ago by
kenneditodd
▴ 10
0
votes
4
replies
1.6k
views
Extra header column stopping EMMAX (C), but not seen in input files
emmax
genomics
Cpp
plink
GWAS
updated 8 days ago by
Ram
39k • written 5.3 years ago by
michael.nagle
▴ 100
1
vote
4
replies
2.5k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl
ortho
ubuntu
mysql
updated 6 days ago by
Ram
39k • written 5.0 years ago by
wocana
▴ 20
3
votes
4
replies
629
views
R package DESeq2 in R 3.5.1
R
updated 19 days ago by
Ram
39k • written 4 months ago by
sehriban.buyukkilic
• 0
1
vote
4
replies
544
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx
differential-expression
t-test
deconvolution
updated 18 days ago by
ATpoint
72k • written 4 weeks ago by
Sam
▴ 280
1
vote
4
replies
807
views
R package error messages have missing package names
R
updated 15 days ago by
Ram
39k • written 20 months ago by
Rahul Tyagi
• 0
1
vote
4
replies
958
views
Simulate the sequence data
next-gen-sequencing
genetics
updated 8 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
0
votes
4
replies
377
views
BCL2 fusions not detected in RNA level
fusion
RNA
BCL2
updated 24 days ago by
ATpoint
72k • written 25 days ago by
J.F.Jiang
▴ 900
1
vote
4
replies
4.8k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R
heatmap
updated 11 days ago by
Ram
39k • written 5.2 years ago by
chetana
▴ 60
0
votes
4
replies
258
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
2 days ago by
Ahmad
▴ 10
1
vote
4
replies
362
views
Bacterial metatransciptome antimicrobial resistance genes workflow?
RNAseq
metatranscriptomics
13 days ago by
SushiRoll
▴ 100
0
votes
4
replies
475
views
BBduk reading fastq from S3 directly - Is it possibile?
BBduk
BBTools
BBMap
9 days ago by
Marko
▴ 10
1
vote
4
replies
265
views
My VCF file structure is strange and less compatible to data processing programs.
VCF
GATK
SNPs
updated 20 days ago by
Istvan Albert
98k • written 20 days ago by
kgwkk2
• 0
1
vote
4
replies
1.5k
views
Time series event recurrence comparison
recurrence
time-series
updated 6 hours ago by
Ram
39k • written 6.7 years ago by
Nicolas Rosewick
10k
12
votes
4
replies
493
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
15 days ago by
Rafael Soler
★ 1.2k
0
votes
4
replies
319
views
SCT transform
scttranform
seurat
updated 26 days ago by
ATpoint
72k • written 27 days ago by
No.Lar037477
▴ 10
0
votes
4
replies
856
views
bowtie2 -all ... multiple alignment Chip-seq
bowtie2
alignment
ChIP-Seq
multiple-alignment
updated 14 days ago by
Ram
39k • written 3.6 years ago by
poltora4enko
▴ 10
0
votes
4
replies
4.8k
views
Sequence alignment length
multiple-sequence-alignment
updated 14 days ago by
Ram
39k • written 6.3 years ago by
biobudhan
▴ 20
1
vote
4
replies
287
views
viewing hgvs in genome data viewer
ncbi
hgvs
clinvar
27 days ago by
curious
▴ 720
0
votes
4
replies
2.1k
views
picard markduplicate output smaller file
picard
markduplicates
gatk
updated 4 days ago by
Ram
39k • written 4.4 years ago by
Peter Chung
▴ 190
2
votes
4
replies
1.3k
views
hisat2 SyntaxError: invalid syntax
alignment
hisat2
updated 15 days ago by
Ram
39k • written 19 months ago by
Xiaoyun
▴ 10
0
votes
4
replies
3.7k
views
What is Dunn's multiple comparison test?
statistics
updated 14 days ago by
Ram
39k • written 5.7 years ago by
Koreanraichu
• 0
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 6 hours ago by
Ram
39k • written 6.8 years ago by
statfa
▴ 720
0
votes
4
replies
499
views
From VCF to BEAGLE format with multiple chromosomes
vcf
vcftools
beagle
gvcf
6 days ago by
Begonia_pavonina
▴ 100
1
vote
4
replies
341
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 2 days ago by
solarchan7
• 0 • written 7 days ago by
survive
• 0
3
votes
4
replies
2.4k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 13 days ago by
Ram
39k • written 2.2 years ago by
roybatty269
• 0
0
votes
4
replies
322
views
csv to custom manifest file
illumina
19 days ago by
bioguy24
▴ 230
510 results • Page
2 of 11
Recent Votes
Answer: How do you add an ORF that overlaps the two regions where a circular genome is c
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Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
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Comment: Unusual FASTQ file
by
Ram
39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ?
by
bhumm
▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file
by
bhumm
▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
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ATpoint
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
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swbarnes2
13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
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39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
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turcoa1
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my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
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Ram
39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
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turcoa1
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129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
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39k
What data are you downloading? Can you show us your GDCquery commands please?
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129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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