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1,000 results • Page
3 of 20
Sort: replies
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Views
Votes
Replies
0
votes
18
replies
1.8k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 8 months ago by
GenoMax
141k • written 8 months ago by
Apex92
▴ 280
14
votes
18
replies
4.9k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 7.3 years ago by
Biostar
20 • written 7.5 years ago by
plink_9857
▴ 50
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
23 days ago by
b.contreras.moreira
▴ 170
0
votes
18
replies
1.9k
views
freebayes error variant calling
snp
3.7 years ago by
evelyn
▴ 230
4
votes
18
replies
4.1k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Joel TM
▴ 60
16
votes
18
replies
5.5k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.7 years ago by
Mensur Dlakic
★ 27k • written 4.7 years ago by
tikshyadav19
• 0
3
votes
18
replies
1.9k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
18 months ago by
lacb
▴ 120
4
votes
18
replies
3.0k
views
Inline barcodes in the reverse reads
barcodes
7.5 years ago by
Picasa
▴ 640
1
vote
18
replies
2.7k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
7.7 years ago by
Tom
▴ 40
20
votes
17
replies
6.0k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.7 years ago by
Anand Rao
▴ 630
7
votes
17
replies
4.3k
views
Strange MA-plot using DESeq2
rna-seq
R
deseq2
updated 7.3 years ago by
Biostar
20 • written 7.4 years ago by
stan
▴ 80
5
votes
17
replies
4.3k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics
encode
10.1 years ago by
14134125465346445
★ 3.6k
5
votes
17
replies
8.5k
views
Removing fastq duplicates
sequence
next-gen
ChIP-Seq
3.4 years ago by
C4
▴ 30
6
votes
17
replies
2.4k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen
assembly
genome
alignment
5.8 years ago by
williamsbrian5064
▴ 510
0
votes
17
replies
3.6k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq
wgcna
software error
R
next-gen
updated 2.3 years ago by
Dio
• 0 • written 5.6 years ago by
giuseppe0525
▴ 20
12
votes
17
replies
4.9k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
6.5 years ago by
anonymous1192976466
▴ 50
7
votes
17
replies
3.9k
views
How to find the differences in aligned bam files
RNA-Seq
7.2 years ago by
1769mkc
★ 1.2k
4
votes
17
replies
2.8k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray
gene-expression
CV
error
4.8 years ago by
Jurat Shahidin
▴ 100
0
votes
17
replies
4.9k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 19 months ago by
Ram
43k • written 8.6 years ago by
jigarnt
▴ 30
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.5 years ago by
dimitrischat
▴ 210
28
votes
17
replies
22k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.4 years ago by
Leite
★ 1.3k
1
vote
17
replies
4.2k
views
Error executing bedops convert2bed
bedops
bed
vcf
convert2bed
7.3 years ago by
lakhujanivijay
5.8k
2
votes
17
replies
2.9k
views
Snakemake Megahit error
megahit
Snakemake
2.4 years ago by
blackadder
▴ 30
20
votes
17
replies
3.2k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by
1769mkc
★ 1.2k • written 3.2 years ago by
pomodoro_sinensis
▴ 110
9
votes
17
replies
2.2k
views
Creating intergenic bam file
R
genome
intergenic
alignment
7.7 years ago by
erincyurtman
• 0
3
votes
17
replies
1.5k
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV
DownSample
fastq
copy number not accurate
4.2 years ago by
lffu_0032
▴ 90
1
vote
17
replies
2.4k
views
Normalizing BLAST results
blast
updated 6.6 years ago by
Biostar
20 • written 6.7 years ago by
db
• 0
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools
relatedness
6.2 years ago by
Sharon
▴ 600
3
votes
17
replies
2.8k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing
faire
mapping
3.1 years ago by
boczniak767
▴ 850
0
votes
17
replies
2.8k
views
Fail running blastdb and blastn on my own computer
blast
6.5 years ago by
annette440
• 0
4
votes
17
replies
2.8k
views
Cufflinks analysis and gffread
RNA-Seq
Assembly
updated 6.5 years ago by
Kevin Blighe
87k • written 6.5 years ago by
qudrat
▴ 100
7
votes
17
replies
6.5k
views
HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
R
gene
genome
5.8 years ago by
WUSCHEL
▴ 750
2
votes
17
replies
9.6k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping
genome
fastq
STAR
updated 2.1 years ago by
todd.ugine
• 0 • written 3.3 years ago by
merfer0206
• 0
0
votes
17
replies
1.1k
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
3 months ago by
Foad
▴ 10
0
votes
17
replies
3.1k
views
I am not able to let R read my file
R
fasta
updated 3.1 years ago by
Arup Ghosh
3.2k • written 3.1 years ago by
trejomarco6
• 0
0
votes
17
replies
1.5k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
3.6 years ago by
Dunois
★ 2.5k
2
votes
17
replies
4.4k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam
bam
alignment
samtools
updated 10.3 years ago by
Devon Ryan
104k • written 10.3 years ago by
Rohit
★ 1.5k
2
votes
17
replies
5.1k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 6.1 years ago by
h.mon
35k • written 6.1 years ago by
Janey
▴ 30
1
vote
17
replies
5.7k
views
BBMap: Mapping Fails
BBTools
BBMap
Mapping
updated 8.1 years ago by
GenoMax
141k • written 8.1 years ago by
cacampbell
▴ 60
7
votes
16
replies
3.6k
views
How do I get a GFF file
snp
4.8 years ago by
apl00028
▴ 90
0
votes
16
replies
4.6k
views
Issue using MaSuRCA-3.2.6
Assembly
assembler
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
Chvatil
▴ 130
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 10 months ago by
Ram
43k • written 4.2 years ago by
Ankit
▴ 500
3
votes
16
replies
3.5k
views
FastTree trifurcating Root node
alignment
FastTree
Phylogenetic Tree
5.3 years ago by
Moses
▴ 150
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X
draft_genome
Assembly
5.7 years ago by
Mostafa
▴ 20
7
votes
16
replies
2.8k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 13 months ago by
Ram
43k • written 6.5 years ago by
Matteo Schiavinato
★ 3.6k
4
votes
16
replies
8.7k
views
STAR - genome indexes generation, genome file not created
RNA-Seq
star
updated 4.6 years ago by
Biostar
20 • written 7.4 years ago by
lu.ne
▴ 70
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene
next-gen
4.3 years ago by
Chaimaa
▴ 260
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.5 years ago by
bioinfo456
▴ 150
0
votes
16
replies
4.3k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 21 months ago by
Ram
43k • written 9.0 years ago by
bharata1803
▴ 560
5
votes
16
replies
2.7k
views
How to extract intron counts from total RNA Sequencing?
featurecounts
RNAseq
htseq
STAR
17 months ago by
PK
▴ 130
1,000 results • Page
3 of 20
Recent Votes
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
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Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
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