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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
0
votes
21
replies
2.8k
views
HTSeq-Count: no_feature too high?
htseq-count
19 months ago by
sea.joson
▴ 10
7
votes
21
replies
3.2k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.5 years ago by
jmsyl.hong
• 0
5
votes
20
replies
4.2k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 20 months ago by
Ram
44k • written 8.7 years ago by
Hans
▴ 140
6
votes
20
replies
6.5k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.9 years ago by
princy149
▴ 80
8
votes
20
replies
2.5k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 24 months ago by
Ram
44k • written 5.8 years ago by
Bara'a
▴ 270
22
votes
20
replies
2.6k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 13 months ago by
Ram
44k • written 7.8 years ago by
Farbod
★ 3.4k
4
votes
20
replies
1.9k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
4.4 years ago by
schlogl
▴ 160
2
votes
20
replies
2.4k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
8 months ago by
Maxine
▴ 40
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
7 months ago by
langziv
▴ 50
8
votes
20
replies
3.0k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
6.4 years ago by
corend
▴ 70
5
votes
20
replies
8.4k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.8 years ago by
varsha619
▴ 90
9
votes
20
replies
4.4k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 14 months ago by
Ram
44k • written 5.8 years ago by
marongiu.luigi
▴ 710
8
votes
20
replies
2.7k
views
Getting read depth for normal and tumour
R
WGS
vcf
5.1 years ago by
zizigolu
★ 4.3k
6
votes
19
replies
2.9k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
4.8 years ago by
aloke205
▴ 40
3
votes
19
replies
1.6k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 10 months ago by
Asaf
10k • written 10 months ago by
captainlabman
▴ 20
18
votes
19
replies
2.3k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 17 months ago by
Ram
44k • written 5.4 years ago by
rbkh09
• 0
4
votes
19
replies
3.2k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 6.7 years ago by
Biostar
20 • written 6.9 years ago by
cool.abbecker
▴ 30
9
votes
19
replies
2.4k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.3 years ago by
schlogl
▴ 160
17
votes
19
replies
2.9k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.7 years ago by
Gian77
▴ 60
22
votes
19
replies
3.2k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.6 years ago by
zizigolu
★ 4.3k
5
votes
19
replies
4.1k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 4 months ago by
ATpoint
82k • written 5.0 years ago by
ta_awwad
▴ 340
10
votes
19
replies
3.5k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 3.0 years ago by
GenoMax
142k • written 3.0 years ago by
matt
▴ 20
15
votes
19
replies
1.9k
views
trimmomaric command for a fasta file?
trimmomatic
updated 6.1 years ago by
Ram
44k • written 6.1 years ago by
Nadin.asal
• 0
0
votes
19
replies
1.4k
views
map fasts files
RNA-Seq
FASTQ
R
6.3 years ago by
Learner
▴ 280
0
votes
19
replies
2.0k
views
scatterplot in R
microarray
expression
gene
updated 19 months ago by
Ram
44k • written 19 months ago by
bioinformatics
▴ 40
1
vote
19
replies
7.1k
views
Conda install package - different internals
R
software error
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
lihe.liu
▴ 30
3
votes
19
replies
6.2k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 5.0 years ago by
finswimmer
16k • written 5.0 years ago by
sruthi
▴ 40
5
votes
19
replies
1.7k
views
how I can come up with a permanent error
R
software error
7.1 years ago by
zizigolu
★ 4.3k
1
vote
19
replies
929
views
Matching transcriptomic data to clinical data
R
updated 3 months ago by
Ram
44k • written 3 months ago by
Azra
▴ 10
7
votes
19
replies
3.0k
views
mapping script process sleeping on server.
alignment
updated 2.0 years ago by
Ram
44k • written 9.2 years ago by
lvogel
▴ 30
6
votes
19
replies
1.7k
views
Fastq header modification
sequence
next-gen
updated 6.2 years ago by
Ram
44k • written 6.2 years ago by
Guillaume
• 0
0
votes
19
replies
3.9k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
6.4 years ago by
jaqx008
▴ 110
0
votes
19
replies
2.8k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
2.8 years ago by
rheab1230
▴ 140
0
votes
19
replies
1.6k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
4.4 years ago by
marongiu.luigi
▴ 710
7
votes
19
replies
7.1k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 2.3 years ago by
Ram
44k • written 9.6 years ago by
mheiser1
▴ 10
13
votes
19
replies
5.4k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.5 years ago by
bioplanet
▴ 60
0
votes
19
replies
9.6k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
5.0 years ago by
seta
★ 1.9k
1
vote
19
replies
2.1k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
5.4 years ago by
eozcan
▴ 10
2
votes
18
replies
6.3k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
7.5 years ago by
Sumit Paliwal
▴ 40
4
votes
18
replies
17k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.5 years ago by
Biostar
20 • written 5.8 years ago by
Shelle
▴ 30
2
votes
18
replies
2.4k
views
I need help in this
gene
weblems
alignment
updated 21 months ago by
Ram
44k • written 8.4 years ago by
efosa15
• 0
3
votes
18
replies
1.9k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
19 months ago by
lacb
▴ 120
0
votes
18
replies
2.0k
views
freebayes error variant calling
snp
3.7 years ago by
evelyn
▴ 230
5
votes
18
replies
6.8k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
4.5 years ago by
michelle.piquet
▴ 60
1
vote
18
replies
1.8k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 4.7 years ago by
Biostar
20 • written 4.7 years ago by
Natasha
▴ 40
4
votes
18
replies
3.0k
views
Inline barcodes in the reverse reads
barcodes
7.6 years ago by
Picasa
▴ 640
0
votes
18
replies
1.7k
views
No gene name after annovar vcf file processing
vcf
annovar
4.6 years ago by
valerie
▴ 100
7
votes
18
replies
8.6k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.3 years ago by
Ram
44k • written 9.5 years ago by
hana
▴ 190
7
votes
18
replies
5.0k
views
Fold change UP and Down in dplyr calculation
R
6.8 years ago by
1769mkc
★ 1.2k
7
votes
18
replies
4.6k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
7.6 years ago by
valerie
▴ 100
1,000 results • Page
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Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
![enter image description here][1] [1]: /media/images/081d73bc-759d-4ea4-8b4c-19a65bfd
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
To give more context on how I generated the explorative UMAP, here are the code I used: # Adding metadata Sample to each Seurat object al…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
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beantkapoor16
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So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
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Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
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GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
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