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449 results • Page
1 of 9
Sort: replies
Rank
Views
Votes
Replies
0
votes
14
replies
772
views
Error using HTSEq_count
HTSeq
python
12 days ago by
felipead66
▴ 110
1
vote
12
replies
3.4k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 22 days ago by
ATpoint
68k • written 5.3 years ago by
SMILE
▴ 170
0
votes
11
replies
486
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 9 days ago by
GenoMax
125k • written 11 days ago by
john
• 0
4
votes
10
replies
3.5k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq
TCGA
updated 4 days ago by
Ram
37k • written 7.7 years ago by
David_emir
▴ 460
0
votes
9
replies
2.7k
views
The soapfuse running problem
soapfuse
updated 21 days ago by
Ram
37k • written 7.7 years ago by
syxbestmayer
▴ 10
0
votes
9
replies
432
views
Running ANNOVAR table_annovar.pl. Error convert2annovar.pl: not found
ANNOVAR
perl
Annotation
VCF
24 days ago by
vvs.hazia
• 0
1
vote
9
replies
520
views
Error after installation of AGAT
Perl
AGAT
17 days ago by
L_bioinfo
• 0
4
votes
8
replies
1.9k
views
Select only sequences that align with X% of a query during blastp search
sequence
blast
alignment
updated 4 days ago by
Ram
37k • written 7.7 years ago by
dago
★ 2.7k
1
vote
8
replies
548
views
Retrieve count table from bam file using genomic coordinates
Sequence
Htseq-count
feature
analysis
counts
updated 18 days ago by
Shred
▴ 990 • written 19 days ago by
L_bioinfo
• 0
4
votes
8
replies
662
views
Proteomic Statistics - FDR vs p-value
FDR
proteomics
t-test
p-value
10 days ago by
bhumm
• 0
0
votes
8
replies
2.3k
views
matchprobes for R
alignment
updated 23 days ago by
Ram
37k • written 7.7 years ago by
gizemtatar
• 0
9
votes
7
replies
697
views
Reference genome location
reference
positions
FASTA
alignment
genome
updated 24 days ago by
barslmn
★ 1.2k • written 29 days ago by
Batel
• 0
1
vote
7
replies
238
views
Downloading NT chunks from NCBI and creating a BLAST database
nucleotide
blast
nt
blastn
database_update.pl
updated 1 day ago by
GenoMax
125k • written 3 days ago by
Vinícius
• 0
3
votes
7
replies
1.9k
views
problem with genome viewer IGV
IGV
mapping
BAM
updated 23 days ago by
GenoMax
125k • written 4.6 years ago by
StudentBio
• 0
1
vote
7
replies
356
views
Segmentation Fault error when running salmon quant
mapping
rnaseq
samon
updated 5 days ago by
Medhat
9.5k • written 5 days ago by
Daniel
• 0
0
votes
7
replies
989
views
WGCNA package in R: dendogram plot error
WGCNA
R
updated 26 days ago by
andres.firrincieli
3.1k • written 6 weeks ago by
Yawo
• 0
1
vote
7
replies
3.0k
views
Blastx false positives
blast
updated 22 days ago by
Ram
37k • written 7.7 years ago by
biobio
▴ 50
2
votes
7
replies
598
views
When I run Trimmomatic, I continue to get an "unknown trimmer" error and cannot figure out how to fix it.
trimmomatic
updated 15 days ago by
Ram
37k • written 16 days ago by
littlemicrobiologist
• 0
0
votes
6
replies
256
views
zero byte files in sratoolkit.3.0.1-ubuntu64
fastq
sra-toolkit
rna-seq
updated 4 days ago by
Ngrin
• 0 • written 5 days ago by
Nemo
• 0
2
votes
6
replies
406
views
Predicting protein fold using known stracture
protein
modeller
prediction
3D
updated 17 days ago by
Michael Dondrup
52k • written 17 days ago by
blur
▴ 270
0
votes
6
replies
4.2k
views
Installing BioLinux 8 on Ubuntu 15.04
ubuntu
biolinux
updated 22 days ago by
Ram
37k • written 7.7 years ago by
waqas.ahmad5231
• 0
0
votes
6
replies
342
views
Comparing the GVF file & VCF file
gvf
dna
vcf
ensembl
ngs
updated 4 days ago by
Ben_Ensembl
★ 2.1k • written 8 days ago by
Alireza
▴ 20
1
vote
6
replies
1.9k
views
Retrieve homologs of certain protein from large database
domain
updated 18 days ago by
Ram
37k • written 7.7 years ago by
biotech
▴ 560
2
votes
6
replies
368
views
Removing individuals and plotting Allele Frequency Difference plots from a vcf file
vcf
updated 10 days ago by
Pierre Lindenbaum
152k • written 10 days ago by
Ollie
• 0
1
vote
6
replies
344
views
Bowtie error when indexing a reference file
bowtie
RNA-seq
updated 11 days ago by
ATpoint
68k • written 12 days ago by
Apex92
▴ 240
3
votes
6
replies
517
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
5 days ago by
TN
• 0
0
votes
6
replies
292
views
SNPs annotation using SnpEff
SNPEff
snp
annotation
VCF.
6 days ago by
Eliza
▴ 10
1
vote
6
replies
351
views
DAVID old version
enrichment
analysis
DAVID
16 days ago by
ziyan
• 0
1
vote
6
replies
4.6k
views
Can one use STAR (splice-aware) to align genomic DNA (non-spliced)
genome
ChIP-Seq
updated 22 days ago by
Gopal
• 0 • written 4.3 years ago by
goodez
▴ 630
0
votes
6
replies
660
views
bowtie2, and python script
and
python
bowtie2
script
updated 21 days ago by
barslmn
★ 1.2k • written 22 days ago by
qudrat.nii
• 0
4
votes
6
replies
756
views
Differentially gene expression multispecies
Expression
Multispecies
Rnaseq
differentially
updated 8 days ago by
Lada
▴ 10 • written 18 months ago by
tiagobellintani
▴ 40
1
vote
6
replies
635
views
error in pipeline installation dependent on numpy version 1.18.5
cnn
numpy
imaging
python
19 days ago by
Omics data mining
▴ 210
1
vote
6
replies
537
views
Get length of the alignment from bam file with shell
NGS
sam
pysam
samtools
bam
updated 23 days ago by
cmdcolin
★ 2.7k • written 23 days ago by
zhangfish
▴ 40
2
votes
5
replies
2.8k
views
QuasiSeq vs. DESeq2 results
deseq2
normalisation
quasiseq
erccdashboard
updated 22 days ago by
Ram
37k • written 7.7 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
5
replies
3.2k
views
Gencode annotation and read counting- how to handle overlapping/ambiguous features
gencode
alignment
RNA-Seq
updated 29 days ago by
Ram
37k • written 7.6 years ago by
Adamc
▴ 670
1
vote
5
replies
490
views
gene ontology of a certain gene names
R
updated 19 days ago by
barslmn
★ 1.2k • written 23 days ago by
Bioinfo
• 0
0
votes
5
replies
556
views
cellranger arc genome build error and how to fix it
canfam4
gtf
cellranger
updated 29 days ago by
Ram
37k • written 4 weeks ago by
josh.mannheimer
• 0
4
votes
5
replies
200
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
error
BAM
Bowtie
updated 1 day ago by
GenoMax
125k • written 2 days ago by
luzglongoria
▴ 40
3
votes
5
replies
6.2k
views
Converting Vcftools output to R readable format
vcf
SNP
R
vcftools
updated 5 days ago by
Ram
37k • written 7.7 years ago by
pifferdavide
▴ 100
1
vote
5
replies
2.5k
views
who can give me the data of genome music bmr calc-covg
genome
music
bmr
calc-covg
updated 4 days ago by
Ram
37k • written 7.7 years ago by
qwertyuiop201320142015
• 0
0
votes
5
replies
2.7k
views
Extracting rRNA sequences from illumina metagenomic dataset
rRNASelector
qiime
Metaxa
updated 19 days ago by
Ram
37k • written 7.7 years ago by
marcelelaux
▴ 20
0
votes
5
replies
1.8k
views
How to increase the speed of miRanda target prediction program?
miranada
mirna
parallel
updated 15 days ago by
Nicolas Rosewick
10k • written 5.2 years ago by
lakhujanivijay
5.7k
1
vote
5
replies
174
views
How to Calulate Allele Frequency from a VCF File?
frequency
allele
VCF
6 hours ago by
Emoji
• 0
0
votes
5
replies
1.7k
views
tools for sequence separation
Assembly
next-gen-sequencing
updated 25 days ago by
Ram
37k • written 7.7 years ago by
mheyda
▴ 20
0
votes
5
replies
398
views
Gene expression annotation for microarray from BiomaRt R package
BiomaRt
gene-expression
R
23 days ago by
Lisa
• 0
1
vote
5
replies
558
views
bamtools split ERROR: could not open mybam.bam for writing.
bam
bamtools
updated 23 days ago by
Ram
37k • written 24 days ago by
GOMATHI NAYAGAM S
• 0
2
votes
5
replies
658
views
comparative transcriptome - how to normalize and analyze DEGs?
RNA-Seq
rna-seq
R
updated 9 days ago by
Lada
▴ 10 • written 2.4 years ago by
nadal-t
▴ 20
0
votes
5
replies
461
views
How to label by colour in PCA plot?
label
PCA
plot.
colure
updated 7 days ago by
seidel
10k • written 7 days ago by
Info.shi
▴ 10
1
vote
5
replies
294
views
convert tsv file to VCF
CADD
vcf
updated 8 days ago by
barslmn
★ 1.2k • written 9 days ago by
Eliza
▴ 10
0
votes
5
replies
2.5k
views
Haplotype phasing and imputation in Beagle 5.1
haplotype-phasing
imputation
Beagle
rehh
updated 12 days ago by
barslmn
★ 1.2k • written 3.3 years ago by
kas
• 0
449 results • Page
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Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Comment: Gene Set Enrichment Analysis, pathway, metabolism
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Popular Question
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maxdlf12
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Teacher
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Pierre Lindenbaum
152k
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LDT
▴ 220
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Comment: How to calculate tumor mutation burden (TMB)?
by
Fabio Marroni
★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
by
Rob
▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers
by
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152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
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I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
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152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
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Pierre Lindenbaum
152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation?
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★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
by
Fabio Marroni
★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file**
by
Pierre Lindenbaum
152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4
by
Pierre Lindenbaum
152k
I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of gzip < chr1.vcf.gz > chr1.vcf.gz…
Comment: Error: unable to open file or unable to determine types for file bed file
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**Error: unable to open file or unable to determine types for file** Hi i am trying to run this commands **bedtools intersect -a Ec_k1…
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Asan Emirsale
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You should find complementary sequences to make the miRNA silent. Should it be the Biopython or another tool. The solution might be as simp…
Comment: counting reads in a fastq file using a refrence fasta file
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vaslanzadeh
▴ 10
Thanks, this works but it is extremely slow, is there any other alternatives?
Answer: HISAT2 output direct to bam sorted
by
ATpoint
68k
hisat2 --dta -x genome -1 ../fastq_zea_mays/SRR214880_1.fastq -2 ../fastq_zea_mays/SRR214880_2.fastq \ | samtools sort -o sorted.b…
Comment: Error: Please supply a reference FASTA/GBK/EMBL file with --reference
by
Neel
▴ 10
Yeah, its working now thank you so much for your reply.
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