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53 results • Page
1 of 2
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0
votes
1
reply
22
views
Fetch Fastq files directly for SRA data
NCBI
FASTQ
SRA
updated 1 hour ago by
Rob
6.2k • written 1 hour ago by
Chintan
• 0
1
vote
2
replies
82
views
Which function is best for pathway analysis?
pathway
1 hour ago by
Chris
▴ 180
0
votes
1
reply
61
views
identify DEGs across all conditions and per specific conditions
R
bulk
DEseq2
updated 2 hours ago by
Yogi
▴ 20 • written 7 hours ago by
camillab.
▴ 130
0
votes
3
replies
60
views
Bug of vg surject
vg
updated 1 hour ago by
Jordan M Eizenga
▴ 360 • written 3 hours ago by
Qi
• 0
0
votes
0
replies
48
views
GO ENRICHMENT ANALYSIS- DESEQ
GO
7 hours ago by
oduduabasi.isaiah
• 0
7
votes
6
replies
342
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
updated 3 hours ago by
dsull
★ 4.7k • written 2 days ago by
Mehwish
• 0
0
votes
1
reply
117
views
Bacterial Pangenome Analysis
Prokka
Pangenome
bacteria
Roary
updated 8 hours ago by
Ram
40k • written 1 day ago by
kirankumareripogu
▴ 10
0
votes
8
replies
339
views
Violin plot (Monocle 3) - Troubleshooting
Monocle3
updated 8 hours ago by
Ram
40k • written 1 day ago by
seattlescientist_01
• 0
1
vote
8
replies
242
views
How to plot proportion of cells in each cluster with scanpy?
scRNA-seq
scanpy
single-cell
10 hours ago by
bioinfo
▴ 110
0
votes
1
reply
83
views
Troubles launch IGV on Linux(Debian)
IGV
updated 7 hours ago by
morovatunc
▴ 550 • written 10 hours ago by
PoscaXVIII
• 0
0
votes
4
replies
163
views
Comparing multiple columns from two files using AWK
awk
updated 11 hours ago by
Ram
40k • written 12 hours ago by
emiliomastriani
▴ 30
0
votes
1
reply
86
views
DESeq2 error - converting result object into dataframe
R
DESeq2
Shiny
updated 12 hours ago by
Ram
40k • written 12 hours ago by
shasabhi1
• 0
0
votes
1
reply
83
views
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
data
Population
with
genetic
HTS
updated 12 hours ago by
Ram
40k • written 12 hours ago by
deorugz
• 0
3
votes
3
replies
2.2k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 13 hours ago by
Ram
40k • written 2.0 years ago by
Anand
▴ 40
0
votes
0
replies
58
views
How to remove chimera from 16S Sanger contigs
sanger-sequencing
chimera
uchime
updated 14 hours ago by
Ram
40k • written 15 hours ago by
eimanpharmacist
▴ 20
2
votes
0
replies
78
views
Herald:
The Biostar Herald for Tuesday, September 26, 2023
herald
16 hours ago by
Biostar
2.0k
0
votes
0
replies
66
views
ptt and rnt files that were created from assembly rather than a genome
rockhopper
genbank
updated 14 hours ago by
Ram
40k • written 16 hours ago by
langziv
▴ 50
0
votes
3
replies
136
views
Running Rockhopper from a command-line
rockhopper
java
updated 14 hours ago by
Ram
40k • written 19 hours ago by
langziv
▴ 50
1
vote
5
replies
167
views
bcftools error merging two VCFs: REF prefixes differ
bcftools
VCF
8 hours ago by
Shane
• 0
0
votes
1
reply
240
views
Gene enrichment analysis of prokaryotes gene
prokaryotes
GO
enrichment
DEG
updated 19 hours ago by
dthorbur
▴ 550 • written 5 days ago by
Genta
• 0
0
votes
1
reply
105
views
GWAS phenotype
R
GWAS
phenotype
updated 20 hours ago by
dthorbur
▴ 550 • written 23 hours ago by
sooni
▴ 10
0
votes
1
reply
219
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics
transcriptome
rsem
ngs
updated 14 hours ago by
biofalconch
▴ 980 • written 20 hours ago by
kat.bi
• 0
0
votes
2
replies
156
views
how to create a loop in R
R
offtopic
updated 14 hours ago by
Ram
40k • written 20 hours ago by
mthm
▴ 50
0
votes
4
replies
157
views
BED files
BED
NGS
Chromosomes
updated 13 hours ago by
Ram
40k • written 21 hours ago by
adarsh_pp
▴ 30
1
vote
5
replies
193
views
How the first sequencing template removed in pair end sequencing
NGS
RNA-seq
WGS
sequence
12 hours ago by
octpus616
▴ 80
0
votes
3
replies
185
views
Saving the output of LD pruning from SNPRelate package as a new GDS file
LD-pruning
SNPRelate
updated 13 hours ago by
James W. MacDonald
▴ 20 • written 1 day ago by
Patrick
• 0
0
votes
2
replies
451
views
Average Coverage after Assembly (Spades)
coverage
average
assembly
updated 23 hours ago by
taniapsduarte
• 0 • written 13 months ago by
davidmaimoun
▴ 50
0
votes
5
replies
710
views
Can vg take MUMmer output as input?
vg
updated 14 hours ago by
Ram
40k • written 2.8 years ago by
ac2278
▴ 20
2
votes
5
replies
1.9k
views
6 follow
Samtools Failing to Install through Conda
samtools
conda
updated 14 hours ago by
Ram
40k • written 17 months ago by
jjp55
▴ 20
3
votes
10
replies
394
views
Should I Learn Docker to Run Command Line Bioinformatics Tool?
Docker
updated 10 hours ago by
ATpoint
76k • written 1 day ago by
arriyaz.nstu
▴ 30
3
votes
2
replies
163
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation
DMR
updated 22 hours ago by
Basti
★ 1.7k • written 1 day ago by
epianalysis
• 0
1
vote
4
replies
223
views
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
ggplot2
ANOVA
t-test
19 hours ago by
RM123
▴ 10
0
votes
1
reply
124
views
Download an example of fully-imputed VCF files ?
VCF
impute
updated 21 hours ago by
barslmn
★ 1.8k • written 1 day ago by
Ben
• 0
7
votes
7
replies
327
views
Filter human transcription factors
transcription-factor
RNA-seq
updated 15 hours ago by
jared.andrews07
★ 15k • written 1 day ago by
Chris
▴ 180
2
votes
5
replies
227
views
obtaining circular RNAs' sequences from circBase
circular-RNA
updated 20 hours ago by
Barry Digby
★ 1.2k • written 1 day ago by
aminijavad4
▴ 10
0
votes
6
replies
239
views
gene correlations in between two groups
gene-expression
correlation
13 hours ago by
biology_inform
▴ 40
2
votes
9
replies
414
views
Calculation of TMB on gene level
genomics
updated 17 hours ago by
svp
▴ 590 • written 1 day ago by
smrutimayipanda
▴ 20
1
vote
5
replies
259
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
14 hours ago by
omer.shomrat
• 0
0
votes
1
reply
189
views
Merging the filename with tsv files for master file
genomics
updated 21 hours ago by
barslmn
★ 1.8k • written 3 days ago by
smrutimayipanda
▴ 20
3
votes
6
replies
326
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
updated 2 hours ago by
Istvan Albert
98k • written 3 days ago by
Athena
• 0
2
votes
5
replies
327
views
How to check RNAseq support for annotated genes?
gene
RNA-seq
annotation
updated 7 hours ago by
Michael
53k • written 4 days ago by
BioinfoBee
• 0
1
vote
5
replies
352
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 22 hours ago by
ATpoint
76k • written 5 days ago by
vk
▴ 40
2
votes
2
replies
241
views
Simulate short-read RNA-seq data from long-read RNA-seq data
polyester
single-cell
simulation
short-read
long-read
16 hours ago by
rhonddaskl
• 0
6
votes
1
reply
168
views
How to retrieve sample informations from given ID from Sequence Read Archives?
eutils
SRA
updated 13 hours ago by
Ram
40k • written 7 days ago by
DareDevil
★ 3.3k
2
votes
8
replies
462
views
Read block operation failed with BAM file
bgzip
samtools
bam
pysam
htslib
updated 19 hours ago by
John Marshall
3.0k • written 8 days ago by
Alex Reynolds
35k
15
votes
6
replies
998
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
18 hours ago by
Rafael Soler
★ 1.2k
0
votes
9
replies
996
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 13 hours ago by
rfran010
▴ 810 • written 12 days ago by
pb11
▴ 10
0
votes
7
replies
916
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 13 hours ago by
rfran010
▴ 810 • written 13 days ago by
ccbb7aab4
▴ 20
0
votes
3
replies
281
views
Assigning GO ids to blast hits
Linux
GO
blast
updated 18 hours ago by
gv
• 0 • written 20 days ago by
Mousumi Akter
• 0
2
votes
13
replies
1.5k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 13 hours ago by
Ram
40k • written 5 weeks ago by
epianalysis
• 0
53 results • Page
1 of 2
Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Answer: Fetch Fastq files directly for SRA data
by
Rob
6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe
by
YUYANG.OON
• 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject
by
Jordan M Eizenga
▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis?
by
Chris
▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject
by
Qi
• 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject
by
Jordan M Eizenga
▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis?
by
Yogi
▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions
by
Yogi
▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question
by
Istvan Albert
98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate
by
dsull
★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian)
by
morovatunc
▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes?
by
Michael
53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate
by
Mehwish
• 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting
by
Ram
40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
bk11
★ 1.2k
I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
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