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1,000 results • Page
3 of 20
Sort: Votes
Rank
Views
Votes
Replies
5
votes
10
replies
781
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
4 weeks ago by
alwayshope
▴ 30
5
votes
11
replies
727
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 6 weeks ago by
cmdcolin
★ 3.2k • written 7 weeks ago by
pablo
▴ 280
5
votes
6
replies
438
views
Calculate the percentage of genomic region covered from the BED file.
NGS
sequencing
genomics
exome
genes
updated 8 weeks ago by
rfran010
▴ 810 • written 8 weeks ago by
adarsh_pp
▴ 30
5
votes
8
replies
662
views
conda: command not found: gatk.
conda
gatk
3 months ago by
bestone
▴ 20
5
votes
7
replies
2.6k
views
download recent list of human exons
human-exons
updated 10 months ago by
Ram
40k • written 8.2 years ago by
Maria333
▴ 20
5
votes
7
replies
417
views
Salmon index not progressing
salmon
updated 4 days ago by
Michael
53k • written 5 days ago by
camillab.
▴ 130
5
votes
7
replies
538
views
About the value in bigwig file
ATAC-seq
updated 11 weeks ago by
rfran010
▴ 810 • written 11 weeks ago by
Chris
▴ 180
5
votes
7
replies
3.2k
views
STAR aligner pauses frequently during mapping
rna-seq
STAR
updated 7 months ago by
Ram
40k • written 8.4 years ago by
E Chen
• 0
5
votes
3
replies
281
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 12 days ago by
Ram
40k • written 12 days ago by
sarahmanderni
▴ 90
5
votes
2
replies
449
views
I want to print only those lines which contain non repetitive amino acid sequences
Linux
python
awk
sed
updated 7 months ago by
Ram
40k • written 7 months ago by
muhammadhassam8
• 0
5
votes
6
replies
3.1k
views
Changes log2FC values of DESeq2
log2FC
DESeq2
updated 6 months ago by
Ram
40k • written 5.8 years ago by
realnewbie
▴ 30
5
votes
4
replies
847
views
Converting Bam file to Fasta (Zipped)
bedtools
samtools
updated 3 months ago by
Ram
40k • written 11 months ago by
Eliveri
▴ 350
5
votes
6
replies
3.1k
views
Can't access DAVID
DAVID
updated 9 months ago by
Ram
40k • written 8.3 years ago by
komal.rathi
★ 4.1k
5
votes
5
replies
432
views
Convert genomic files from known Gigabases(# of bases) to gigabytes
gigabases
gigabytes
genomics
updated 7 months ago by
GenoMax
134k • written 7 months ago by
datanerd
▴ 520
5
votes
6
replies
1.2k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools
bam
bed
updated 3 months ago by
Ram
40k • written 10 months ago by
Eliveri
▴ 350
5
votes
2
replies
2.9k
views
Cut & run - bowtie2 dovetail option
cut and run
dovetail
bowtie2
updated 7 months ago by
baijiangshan9726
• 0 • written 2.9 years ago by
blur
▴ 280
5
votes
7
replies
623
views
RNAseq analysis of phage infection - should I split the counts mapping to host/phage prior to normalization and analysis?
RNAseq
Prokaryotic
5 months ago by
Sean
▴ 10
5
votes
4
replies
3.4k
views
gender SNP marker
SNP
updated 10 months ago by
Ram
40k • written 8.2 years ago by
erezts
• 0
5
votes
2
replies
479
views
30 bp sequence that does not show hit within a genome
similarity
updated 8 months ago by
shenwei356
8.2k • written 8 months ago by
GR
▴ 400
5
votes
7
replies
751
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq
sequencing
updated 4 months ago by
supernovamik
• 0 • written 3.7 years ago by
ee.mohseni.alert
▴ 50
5
votes
9
replies
2.6k
views
differential expression analysis tools for single end reads
rna-seq
next-gen
updated 11 months ago by
Ram
40k • written 8.1 years ago by
mike
▴ 90
5
votes
8
replies
1.1k
views
snpeff install error
snpeff
updated 4 months ago by
Ram
40k • written 4 months ago by
bestone
▴ 20
5
votes
6
replies
866
views
I can not allocate ram memory for WSL2
WSL2
6 months ago by
ailton
• 0
5
votes
7
replies
1.1k
views
error while using cyvcf2 to parse the vcf file
cyvcf2
vcf
htslib
updated 4 months ago by
Ram
40k • written 16 months ago by
rheab1230
▴ 140
5
votes
8
replies
1.6k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 9 weeks ago by
Jordan M Eizenga
▴ 360 • written 8 months ago by
TN
• 0
5
votes
4
replies
939
views
Running nf-core rnaseq with smart-seq3 data
smart-seq3
nf-core
nextflow
9 months ago by
firestar
★ 1.6k
5
votes
5
replies
1.6k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 4 months ago by
Ram
40k • written 5.7 years ago by
wizofe
• 0
5
votes
1
reply
313
views
Enricher with Gene Symbols
DGE
ClusterProfiler
Enrich
ORA
updated 6 weeks ago by
bk11
★ 1.2k • written 6 weeks ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
20
replies
3.6k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 12 months ago by
Ram
40k • written 8.1 years ago by
Hans
▴ 140
5
votes
6
replies
525
views
normalize coordinates to the same length
r
genomicranges
5 months ago by
Chironex
▴ 40
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 3 months ago by
Ram
40k • written 7.2 years ago by
statfa
▴ 740
5
votes
3
replies
872
views
abyss-pe genome assembly
konnector
abyss-pe
updated 3 months ago by
Ram
40k • written 4.6 years ago by
Igor Lalin
• 0
5
votes
9
replies
3.7k
views
Combining all biological replicates
RNA-Seq
Cuffdiff
updated 11 months ago by
Ram
40k • written 8.1 years ago by
melati
▴ 10
5
votes
4
replies
3.8k
views
Black color reads in IGV: bwa-meth
IGV
alignment
bwa-meth
updated 8 months ago by
Ram
40k • written 8.3 years ago by
mehran.karimzade
▴ 220
5
votes
6
replies
1.2k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2
R
RNA-Seq
updated 3 months ago by
Ram
40k • written 3.4 years ago by
Ranan Jyoti Sarma
▴ 80
5
votes
35
replies
2.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 11 weeks ago by
Jordan M Eizenga
▴ 360 • written 3 months ago by
anivlete
• 0
5
votes
12
replies
879
views
Data from an experiment
single-cell
updated 7 months ago by
GenoMax
134k • written 7 months ago by
Chris
▴ 180
5
votes
11
replies
558
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 7 weeks ago by
Ram
40k • written 7 weeks ago by
Chris
▴ 180
5
votes
11
replies
3.3k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 6 months ago by
Ram
40k • written 5.4 years ago by
HG
▴ 30
4
votes
4
replies
698
views
Where can I find the genetic map for GRCh37 to phase genotypes on SHAPEIT2
genetics
genetic
map
shapeit2
11 months ago by
Khaleesi95
▴ 40
4
votes
5
replies
458
views
STAR mapping - regarding output files content
STAR
RNA-seq
mapping
updated 5 weeks ago by
rfran010
▴ 810 • written 6 weeks ago by
Manko47
• 0
4
votes
6
replies
880
views
Get transcription factor motif from list of gene symbols
motif
factor
R
transcription
updated 11 months ago by
Matthias Zepper
4.1k • written 11 months ago by
Trivas
★ 1.4k
4
votes
7
replies
2.5k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 6 months ago by
Ram
40k • written 2.2 years ago by
mathavanbioinfo
▴ 70
4
votes
5
replies
774
views
Need help to perform survival analysis
survival
analysis
mirna
updated 6 months ago by
Mensur Dlakic
★ 25k • written 6 months ago by
Bhanu
• 0
4
votes
10
replies
746
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
4 weeks ago by
Y
• 0
4
votes
3
replies
746
views
HaplotypeCaller: GVCF-Mode or VCF for variant calling of single sample?
haplotypecaller
vcf
gatk
gvcf
8 months ago by
DavidStreid
▴ 90
4
votes
9
replies
7.9k
views
bcftools consensus command
vcf
bcftools
updated 6 months ago by
Ram
40k • written 3.7 years ago by
Begonia_pavonina
▴ 100
4
votes
6
replies
1.9k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 3 months ago by
minakshiboruahassam
• 0 • written 13 months ago by
Plus
▴ 20
4
votes
2
replies
449
views
Analyzing bulk RNA-seq
RNAseq
updated 7 months ago by
swbarnes2
13k • written 7 months ago by
Zaid
• 0
4
votes
7
replies
3.8k
views
DEseq with 3 replicates and two conditions
RNA-Seq
updated 11 months ago by
Ram
40k • written 8.1 years ago by
S
▴ 20
1,000 results • Page
3 of 20
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
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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
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▴ 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…
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by
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• 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
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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…
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Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
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Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
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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…
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by
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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 …
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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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