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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
6
votes
4
replies
6.3k
views
What is gnomAD allele frequency
AF
gnomAD
updated 10 weeks ago by
Lhl
▴ 760 • written 3.0 years ago by
Eric Wang
▴ 50
6
votes
5
replies
646
views
Log2 transformation is well used, but is there a good paper that can be used as reference ?
TPM
log2-transformation
r
updated 12 weeks ago by
Kevin Blighe
87k • written 12 weeks ago by
JACKY
▴ 130
6
votes
3
replies
782
views
trimmomatic and STAR alignments
trimmomatic
STAR
RNAseq
sequencing
reads
updated 10 months ago by
stuart archer
▴ 140 • written 11 months ago by
hamarillo
▴ 70
5
votes
4
replies
621
views
FASTQ to BAM to CRAM to FASTQ
Samtools
5 months ago by
ManuelDB
▴ 80
5
votes
35
replies
3.5k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 8 months ago by
Jordan M Eizenga
▴ 460 • written 9 months ago by
anivlete
• 0
5
votes
5
replies
514
views
Generate BED file
bed
7 weeks ago by
daffodil
▴ 10
5
votes
4
replies
1.6k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 10 months ago by
Ram
43k • written 7.7 years ago by
statfa
▴ 750
5
votes
7
replies
771
views
About the value in bigwig file
ATAC-seq
updated 8 months ago by
rfran010
▴ 900 • written 8 months ago by
Chris
▴ 260
5
votes
10
replies
1.2k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
7 months ago by
alwayshope
▴ 40
5
votes
7
replies
865
views
Salmon index not progressing
salmon
updated 6 months ago by
Michael
54k • written 6 months ago by
camillab.
▴ 160
5
votes
6
replies
738
views
Calculate the percentage of genomic region covered from the BED file.
NGS
sequencing
genomics
exome
genes
updated 8 months ago by
rfran010
▴ 900 • written 8 months ago by
adarsh_pp
▴ 40
5
votes
11
replies
1.2k
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 7 months ago by
cmdcolin
★ 3.7k • written 7 months ago by
pablo
▴ 300
5
votes
3
replies
978
views
abyss-pe genome assembly
konnector
abyss-pe
updated 9 months ago by
Ram
43k • written 5.1 years ago by
Igor Lalin
• 0
5
votes
5
replies
599
views
Normalization and Genome-Wide Comparisons with Chipseq
chip-seq
Chipseq
Normalization
updated 3 months ago by
Ankit
▴ 500 • written 3 months ago by
zbeddingfield3
▴ 10
5
votes
7
replies
1.4k
views
error while using cyvcf2 to parse the vcf file
cyvcf2
vcf
htslib
updated 10 months ago by
Ram
43k • written 22 months ago by
rheab1230
▴ 140
5
votes
6
replies
1.4k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2
R
RNA-Seq
updated 9 months ago by
Ram
43k • written 3.9 years ago by
Ranan Jyoti Sarma
▴ 90
5
votes
1
reply
663
views
Learning Linux advance commands
grep
awk
linux
sed
updated 5 months ago by
Zhitian Wu
▴ 60 • written 17 months ago by
rheab1230
▴ 140
5
votes
7
replies
923
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq
sequencing
updated 10 months ago by
supernovamik
• 0 • written 4.2 years ago by
ee.mohseni.alert
▴ 50
5
votes
8
replies
1.8k
views
snpeff install error
snpeff
updated 10 months ago by
Ram
43k • written 11 months ago by
bestone
▴ 30
5
votes
3
replies
287
views
samtools view: error reading file
samtools
bowtie2
updated 22 days ago by
bioinfo_ga
▴ 70 • written 24 days ago by
ray
• 0
5
votes
10
replies
812
views
Error when viewing a bam file
samtools
updated 9 months ago by
Ram
43k • written 11 months ago by
Chris
▴ 260
5
votes
8
replies
2.3k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 8 months ago by
Jordan M Eizenga
▴ 460 • written 14 months ago by
TN
• 0
5
votes
1
reply
585
views
Enricher with Gene Symbols
DGE
ClusterProfiler
Enrich
ORA
updated 7 months ago by
bk11
★ 2.2k • written 7 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
4
replies
1.1k
views
Converting Bam file to Fasta (Zipped)
bedtools
samtools
updated 9 months ago by
Ram
43k • written 17 months ago by
Eliveri
▴ 350
5
votes
3
replies
884
views
GENE code ID conversion
ensembl
entrez
11 months ago by
Confused_human
▴ 20
5
votes
19
replies
3.9k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 3 months ago by
ATpoint
81k • written 4.8 years ago by
ta_awwad
▴ 340
5
votes
7
replies
825
views
RNAseq analysis of phage infection - should I split the counts mapping to host/phage prior to normalization and analysis?
RNAseq
Prokaryotic
11 months ago by
Sean
▴ 10
5
votes
5
replies
472
views
Example MAF Files
MAF
updated 3 months ago by
Ram
43k • written 3 months ago by
anasjamshed
▴ 120
5
votes
8
replies
1.9k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 5 months ago by
Jingjingzhang
• 0 • written 3.6 years ago by
from the mountains
▴ 230
5
votes
5
replies
586
views
Counting 705 fasta header characters ('>') in human genome
human-genome
genetics
updated 5 months ago by
ATpoint
81k • written 5 months ago by
10mz1
▴ 10
5
votes
3
replies
549
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 4 months ago by
cmdcolin
★ 3.7k • written 4 months ago by
dariober
14k
5
votes
7
replies
3.1k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 5 months ago by
Istvan Albert
100k • written 5.8 years ago by
chris.bird
▴ 10
5
votes
5
replies
2.4k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 4 months ago by
Feng Tian
▴ 20 • written 5.5 years ago by
gewa
▴ 20
5
votes
8
replies
531
views
Multiple threads on ubuntu server
Ubuntu
updated 10 weeks ago by
colindaven
6.3k • written 10 weeks ago by
oghzzang
▴ 50
5
votes
11
replies
942
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 7 months ago by
Ram
43k • written 7 months ago by
Chris
▴ 260
5
votes
6
replies
727
views
normalize coordinates to the same length
r
genomicranges
11 months ago by
Chironex
▴ 40
5
votes
2
replies
844
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 5 months ago by
yhdist
▴ 70 • written 6 months ago by
Cookin
▴ 10
5
votes
3
replies
496
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 6 months ago by
Ram
43k • written 6 months ago by
sarahmanderni
▴ 100
5
votes
6
replies
1.6k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools
bam
bed
updated 9 months ago by
Ram
43k • written 17 months ago by
Eliveri
▴ 350
5
votes
8
replies
979
views
sc-RNA seq pipeline
scRNA-seq
NGS
RNA-Seq
11 weeks ago by
subhiksha
▴ 30
5
votes
5
replies
1.8k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 10 months ago by
Ram
43k • written 6.2 years ago by
wizofe
• 0
5
votes
1
reply
655
views
Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance
vg
pggb
giraffe
updated 5 months ago by
Jordan M Eizenga
▴ 460 • written 5 months ago by
Kyran
▴ 30
4
votes
6
replies
1.5k
views
Determining inhouse cut offs
coverage
updated 11 months ago by
Ram
43k • written 7.7 years ago by
skbrimer
▴ 730
4
votes
2
replies
436
views
KEGG DATABASE
DATABASE
KEGG
updated 3 months ago by
jv
★ 1.7k • written 3 months ago by
Sijjil
• 0
4
votes
8
replies
1.9k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 9 months ago by
Ram
43k • written 4.5 years ago by
Kumar
▴ 120
4
votes
12
replies
3.4k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 2 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
3
replies
565
views
Therapy response for multiple cancer types
cancer
dataset
expression
gene
therapy
response
11 months ago by
ysnuye
▴ 20
4
votes
5
replies
508
views
Which refseq_protein db to choose for zingiberaceae
local
blastp
blast
updated 7 months ago by
GenoMax
140k • written 7 months ago by
Nilo
• 0
4
votes
5
replies
2.0k
views
Whole blood single cell RNA-seq dataset?
RNA-Seq
scRNA-Seq
whole blood
single cell
11 months ago by
predeus
★ 1.9k
4
votes
6
replies
777
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
10 months ago by
natalev
▴ 20
1,000 results • Page
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Recent Votes
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You should use `cat` on .gz files, part of the magic of .gz ...I guess if you use `zcat` they are unzipped and this is why you get the erro…
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thank you !!
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Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
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Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
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Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
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You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
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Share code and an example please.
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I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
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