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853 results • Page
2 of 18
Sort: Views
Rank
Views
Votes
Replies
0
votes
8
replies
4.1k
views
Downloading single cell data from NCBI
ncbi
rna-seq
fastq-dump
single-cell
updated 28 days ago by
Ram
40k • written 4.8 years ago by
V
▴ 360
2
votes
7
replies
4.0k
views
GERP++ (gerpcol) error on a test data
GERP
updated 23 hours ago by
Diana
• 0 • written 7.1 years ago by
kirill1984
▴ 10
3
votes
4
replies
4.0k
views
Atypical volcano plot RNA-seq
volcano-plot
RNA-seq
deseq2
updated 28 days ago by
Ram
40k • written 4.9 years ago by
Teresa
▴ 20
8
votes
7
replies
3.9k
views
Problem in indexing toplevel genome with HISAT2
RNA-Seq
genome
hisat2
hisat2-build
index
updated 22 days ago by
Apex92
▴ 270 • written 4.6 years ago by
Batu
▴ 240
2
votes
2
replies
3.6k
views
Insert size is so small, good or bad?
Insert-size
RNA-Seq
updated 15 days ago by
Ram
40k • written 5.9 years ago by
Tania
▴ 180
3
votes
11
replies
3.4k
views
6 follow
Inconsistencies between RNA Seq and PCR
PCR
RNA-Seq
updated 28 days ago by
Ram
40k • written 7.4 years ago by
Bnf83
▴ 150
9
votes
8
replies
3.4k
views
bcftools multiallelic split not working
bcftools
vcf
updated 20 days ago by
DareDevil
★ 3.3k • written 2.1 years ago by
from the mountains
▴ 220
4
votes
12
replies
3.4k
views
6 follow
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 9 days ago by
alejandrogzi
▴ 30 • written 3.4 years ago by
William
★ 5.2k
11
votes
7
replies
3.4k
views
7 follow
Assembler for only nanopore data
genomics
Assembly
ONT
Abyss
updated 10 days ago by
GenoMax
134k • written 4.4 years ago by
ringourquia
▴ 20
5
votes
6
replies
3.3k
views
Tophat's Mean Inner Distance between Mate Pairs
tophat
RNA-seq
updated 28 days ago by
Ram
40k • written 7.9 years ago by
english.server
▴ 290
7
votes
15
replies
3.3k
views
Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index
next-gen
sequencing
updated 2 days ago by
Gabriel R.
★ 2.9k • written 3.3 years ago by
Rezenman
• 0
1
vote
6
replies
3.2k
views
Extracting sequence, not reads, by position from bam
sequence
updated 1 day ago by
manu
• 0 • written 5.0 years ago by
geneware
▴ 10
7
votes
6
replies
3.2k
views
CWL: word counting
Common-Workflow-Language
cwl
updated 10 days ago by
Ram
40k • written 6.3 years ago by
gultagr
▴ 10
10
votes
18
replies
3.1k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 21 days ago by
Ram
40k • written 15 months ago by
reany
▴ 50
0
votes
1
reply
2.9k
views
PSMC plot (Effective population size)
next-gen
updated 22 days ago by
1601693223
• 0 • written 7.8 years ago by
vicky
▴ 30
8
votes
2
replies
2.9k
views
How to edit fasta headers to keep only ID and organism?
fasta
updated 13 hours ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
4
votes
4
replies
2.9k
views
How to keep the top hits only in the output file of hmmscan?
hmmer
hmmscan
updated 13 hours ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
60
votes
21
replies
2.8k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome
assembly
updated 20 days ago by
Michael
53k • written 21 days ago by
sqshigg
▴ 60
0
votes
1
reply
2.8k
views
RNA-seq compare FPKM's or fold change of different organisms
gene-expression
FPKM
RNA-seq
fold-change
updated 6 days ago by
Ram
40k • written 6.1 years ago by
jehu
▴ 30
3
votes
1
reply
2.8k
views
CWL bwa create index to bwa mem alignment workflow
Common-Workflow-Language
CWL
updated 10 days ago by
Ram
40k • written 6.1 years ago by
Biowoogles
▴ 20
2
votes
4
replies
2.8k
views
Bacterial morphology details
bacteria
shape
respiration
updated 27 days ago by
predeus
★ 1.9k • written 8.7 years ago by
Prasad
★ 1.6k
5
votes
4
replies
2.7k
views
Distance Tree For Gerp
conservation
phylogeny
updated 7 days ago by
Diana
• 0 • written 11.6 years ago by
Darked89
4.4k
5
votes
8
replies
2.7k
views
Difference between total number of reads in fastq file and no of bases/nt sequences in fastq file?
FASTQ
updated 2 days ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
0
votes
7
replies
2.6k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 6 days ago by
Ram
40k • written 5.3 years ago by
AP
▴ 80
2
votes
2
replies
2.6k
views
Tools to create flanking sequences for variants based on a VCF file and reference genome.
vcf
assay
updated 8 days ago by
estpallag
▴ 10 • written 7.2 years ago by
William
★ 5.2k
4
votes
6
replies
2.6k
views
IDT vs primer 3 - PCR dimerisation
PCR
primer3
IDT
primer
updated 6 days ago by
Emrah
• 0 • written 3.1 years ago by
timothy.kirkwood
▴ 130
0
votes
3
replies
2.6k
views
Circos plot for ecoli genome
rna-seq
circos
updated 28 days ago by
Ram
40k • written 6.8 years ago by
raya.girish
▴ 30
2
votes
7
replies
2.6k
views
CWL: Getting output file of a CommandLineTool using glob
Common-Workflow-Language
cwl
updated 10 days ago by
Ram
40k • written 5.2 years ago by
skanwal
▴ 50
1
vote
1
reply
2.5k
views
trinity assembly error, run failed
trinity
rna-seq
updated 28 days ago by
Ram
40k • written 7.3 years ago by
nikelle.petrillo
▴ 110
8
votes
7
replies
2.4k
views
6 follow
LncRNA Differential Expression and Analysis of lncRNA and mRNA co-expression.
RNA-Seq
alignment
co-expression
lncRNA
DESeq2
updated 20 days ago by
AS-git
• 0 • written 5.0 years ago by
conor93
▴ 70
5
votes
2
replies
2.4k
views
CWL: Comments in Common Workflow Language
Common-Workflow-Language
cwl
updated 10 days ago by
Ram
40k • written 6.4 years ago by
kevin.o.oluoch
▴ 70
1
vote
1
reply
2.4k
views
SNPhylo Error Help: there is no SNP and Na/NaN arguement
snphylo
tree
VCF
phylogenetic
updated 16 days ago by
GenoMax
134k • written 7.1 years ago by
N Smith
▴ 10
2
votes
6
replies
2.4k
views
hisat2 :Killed (ERR): hisat2-align exited with value 137
RNA-seq
alignment
hisat2
updated 27 days ago by
Ram
40k • written 21 months ago by
iamsmor
• 0
8
votes
7
replies
2.3k
views
CWL rerunning completed output
Common-Workflow-Language
CWL
updated 10 days ago by
Ram
40k • written 6.1 years ago by
bruce.moran
▴ 950
1
vote
1
reply
2.3k
views
CWL: Linker error doing 'pip install cwlref-runner' on CentOS 6 system
cwl
centos6
centos
Common-Workflow-Language
pip
updated 10 days ago by
Ram
40k • written 6.3 years ago by
Kevin Ernst
• 0
2
votes
1
reply
2.3k
views
CWL: Arguments vs Inputs in CommandLineTool.
Common-Workflow-Language
CWL
updated 10 days ago by
Ram
40k • written 5.9 years ago by
mkher
▴ 50
4
votes
2
replies
2.3k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 16 days ago by
GenoMax
134k • written 3.4 years ago by
ATpoint
76k
0
votes
1
reply
2.3k
views
how to read h5 file in Seurat if its structure is not like 10x h5 file structure?
RNA-Seq
single-cell
scRNA-seq
Seurat
R
updated 27 days ago by
Ram
40k • written 21 months ago by
fifty_fifty
▴ 60
3
votes
4
replies
2.2k
views
Heatmap2 missing some genes
heatmap
RNA-seq
updated 28 days ago by
Ram
40k • written 3.5 years ago by
ovariohisterectomia
▴ 40
1
vote
12
replies
2.2k
views
Confused about % of mapped and unmapped reads output from STAR aligner
RNAseq
STAR
updated 7 days ago by
Ram
40k • written 10 months ago by
mohsamir2016
▴ 30
0
votes
7
replies
2.1k
views
How to perform gene annotation in kallisto?
Gene
kallisto
annotation
updated 29 days ago by
호성
• 0 • written 2.1 years ago by
synat.keam
▴ 80
3
votes
7
replies
2.1k
views
Corrupted FASTq files with missing "+" under some sequences.
fastq
RNAseq
corruption
recover
updated 12 days ago by
Tommaso
• 0 • written 2.3 years ago by
akh22
▴ 90
0
votes
3
replies
2.0k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 1 day ago by
aishwarya
• 0 • written 5.2 years ago by
blooming.daisy333
▴ 110
6
votes
4
replies
2.0k
views
CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
Common-Workflow-Language
CWL
updated 10 days ago by
Ram
40k • written 4.0 years ago by
skanwal
▴ 50
5
votes
8
replies
2.0k
views
Distinguish between forward strand, plus strand, sense strand
pysam
strand
star
sam
updated 17 days ago by
Buwei
• 0 • written 14 months ago by
tien
▴ 10
2
votes
7
replies
2.0k
views
PLINK --geno and --mind
PLINK
COVID-19
updated 15 days ago by
karthivalarmathi99
▴ 10 • written 8 months ago by
Ryon
• 0
75
votes
18
replies
2.0k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 3 days ago by
Ram
40k • written 7 days ago by
Kenny
▴ 30
0
votes
2
replies
1.9k
views
CWL :File created on fly by one step of a workflow as input to another step
Common-Workflow-Language
CWL
updated 10 days ago by
Ram
40k • written 6.5 years ago by
akashmdr90
• 0
1
vote
4
replies
1.9k
views
Using ExomeDepth for GRCH38 processed samples to call CNVs
Exome
GrCh38
ExomeDepth
CNV
updated 2 days ago by
Joel Wallenius
▴ 180 • written 2.6 years ago by
nkausthu
▴ 30
2
votes
7
replies
1.9k
views
Issues Phasing with Eagle v2.4
h19
vcf
phasing
eaglev2.4
haplotype
updated 23 days ago by
Robert
• 0 • written 20 months ago by
Francisco
• 0
853 results • Page
2 of 18
Recent Votes
Answer: Assistance with Fungal Genome Annotation Using Maker and BLAST
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Comment: Salmon index not progressing
Answer: Adding a control sample to bulk RNA-seq
Comment: Adding a control sample to bulk RNA-seq
Comment: kallisto normalized TPM values without bootstraps
Comment: Identify Alternative Splicing Event using exon and junction count table
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Comment: Find potential important genes from bulk-RNA seq experiment
by
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53k
You can use e.g. the WGCNA package for network analysis. In your case multiple samples this might mean multiple patients or a time series o…
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
edoardoscali.93
• 0
Thank you so much for your responses. @genomax , I've downloaded both of the databases you recommended. I attempted to combine them into …
Answer: Simulate short-read RNA-seq data from long-read RNA-seq data
by
Mensur Dlakic
★ 24k
I think you could try doing this, but it wouldn't be appropriate. You'd be bringing long-read errors, which I believe are higher than short…
Comment: Salmon index not progressing
by
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▴ 130
I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
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Chris
▴ 180
Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
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13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
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13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
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ATpoint
76k
You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
by
ATpoint
76k
If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
by
camillab.
▴ 130
Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
Comment: Filtering VCF to divide with equal sizes
by
Ram
40k
A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
by
avelarbio46
▴ 30
I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
Comment: Salmon index not progressing
by
ATpoint
76k
Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
Comment: Salmon index not progressing
by
GenoMax
134k
> 2 hrs trying to generate decoy-aware transcriptome for human. is this time normal? It is probably normal considering resources you have…
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
by
grant.hovhannisyan
★ 2.5k
you expect to have aneuploidy only in the knockout?
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