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1,000 results • Page
5 of 20
Sort: replies
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Views
Votes
Replies
4
votes
15
replies
4.0k
views
Paired-read alignment length from BAM/SAM file
bam
sam
paired-read
alignment
6.9 years ago by
Soumitra Pal
▴ 10
5
votes
15
replies
1.6k
views
NGS Sequencing depths
next-gen
sequencing
gene
7.3 years ago by
sliproach
▴ 10
3
votes
15
replies
3.2k
views
Less and less genes predicted with each iteration of SNAP/MAKER
maker
annotation
snap
gene prediction
genomics
updated 2.7 years ago by
jaredbernard
▴ 30 • written 4.1 years ago by
mrmrwinter
▴ 30
1
vote
15
replies
2.0k
views
Samtools merge Illumina and PB bam file empty
Illumina
samtools
Bam
PacBio
updated 14 months ago by
Ram
43k • written 3.8 years ago by
talbots
▴ 30
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
5 months ago by
analyst
▴ 50
6
votes
15
replies
2.7k
views
Why can't I reproduce the same heat map
ggplots
R
RNA-Seq
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
Za
▴ 140
6
votes
15
replies
1.6k
views
The Best Cloud Solution For Genomics
cloud
data-sharing
genomics
workflow
updated 22 months ago by
Ram
43k • written 23 months ago by
davidmaimoun
▴ 50
0
votes
15
replies
3.3k
views
how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
RNA-Seq
6.6 years ago by
genya35
▴ 40
10
votes
15
replies
6.3k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 14 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
20
votes
15
replies
30k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 21 months ago by
Ram
43k • written 8.4 years ago by
dam4l
▴ 200
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling
bcftools
nf-core
10 months ago by
Chris
▴ 280
1
vote
15
replies
3.4k
views
How to perform multiple alignment using MAFFT?
genome
alignment
gene
sequence
3.1 years ago by
anikcropscience
▴ 230
2
votes
15
replies
4.2k
views
How to interpret reads mapped to genome from samtools flagstat vs TopHat align_summary.txt ?
RNA-Seq
8.1 years ago by
Vasu
▴ 770
4
votes
15
replies
3.3k
views
Adding Multiple readgroups to BAM file
GATK
ReadGroups
8.1 years ago by
vakul.mohanty
▴ 270
2
votes
15
replies
1.6k
views
from protein to tRNA combinations
RNA-Seq
rna-seq
written 3.4 years ago by
shiningsky000
• 0
5
votes
15
replies
2.1k
views
Sample contamination level over 30%
next-gen
6.6 years ago by
haiying.kong
▴ 360
1
vote
15
replies
3.7k
views
Install Lefse in Ubuntu 12
install
lefse
microbiome
5.9 years ago by
goh
▴ 10
2
votes
15
replies
1.6k
views
How to call all the allele in samples
SNP
6.1 years ago by
Kritika
▴ 260
1
vote
15
replies
3.8k
views
Fastx quality filter
next-gen
RNA-Seq
software error
sequencing
updated 7.4 years ago by
Ram
43k • written 7.4 years ago by
kriti.awasthi23
▴ 10
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
7.5 years ago by
Farbod
★ 3.4k
0
votes
15
replies
3.7k
views
Identify genes in a tophat aligned bam/sam file
blast
alignment
rna-seq
gene
updated 17 months ago by
Ram
43k • written 8.9 years ago by
gchaves
• 0
7
votes
15
replies
2.1k
views
cufflinks in loop
rna-seq
RNA-Seq
genome
updated 5.9 years ago by
finswimmer
16k • written 5.9 years ago by
suny.bio
• 0
1
vote
15
replies
4.4k
views
Ultrafast alignment of short sequences to a genome (with up to 5 mismatches!)
genome
alignment
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
Aurelie MLB
▴ 360
6
votes
15
replies
1.6k
views
Reads partly within an exon
RNA-Seq
6.8 years ago by
benjyrolls
▴ 70
0
votes
15
replies
2.2k
views
Chromosome accession numbers correspond to which chromosome?
bam
chromosome
bed
18 months ago by
amy__
▴ 160
7
votes
15
replies
7.2k
views
6 follow
blastn error - NCBI C++ Exception
assembly
blast
alignment
updated 2.1 years ago by
lieven.sterck
15k • written 3.1 years ago by
sunnykevin97
▴ 980
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq
differential expression
4.6 years ago by
guillaume.rbt
★ 1.0k
7
votes
15
replies
2.2k
views
very low coverage when mappin genomic DNA
mapping
coverage
DNA
genomic
updated 2.7 years ago by
ATpoint
82k • written 2.7 years ago by
Lila M
★ 1.2k
6
votes
15
replies
2.5k
views
processing in strelka2 with multiples bam file in directory
strelka2
updated 2.4 years ago by
aldhairmedico
▴ 70 • written 4.4 years ago by
bioguy24
▴ 230
2
votes
15
replies
2.2k
views
to get each covariate with PC loading in PCA
RNA-seq
PCA
5.4 years ago by
Grace_G
▴ 20
2
votes
15
replies
4.1k
views
Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
next-gen
SNP
alignment
updated 4.1 years ago by
wm
▴ 560 • written 4.1 years ago by
shrutidabral
▴ 10
5
votes
15
replies
1.5k
views
Get list of gene signatures published
bailey
genes
subtype
pancreas
3.3 years ago by
sabin
▴ 50
3
votes
15
replies
2.8k
views
fastq reads with primers and truseq indexed adapter
sequencing
next-gen
sequence
7.2 years ago by
jomo018
▴ 720
2
votes
14
replies
1.1k
views
heatmap for HTSeq data in R
RNA-Seq
updated 3.5 years ago by
Ram
43k • written 3.5 years ago by
Rob
▴ 170
1
vote
14
replies
2.0k
views
Counts all read zero after alignment?
alignment
rna-seq
updated 23 months ago by
Ram
43k • written 2.7 years ago by
tul66893
• 0
5
votes
14
replies
1.7k
views
Interpretation for lowfrevariant
vcf
6.3 years ago by
Tania
▴ 180
2
votes
14
replies
1.9k
views
Issue with replicating from a research paper-motifs
sequence
RNA
FASTA
MEME
motif
updated 5.0 years ago by
GouthamAtla
12k • written 5.0 years ago by
joshua.steier
▴ 20
0
votes
14
replies
1.9k
views
analyzing cel files
chip
snp
updated 2.8 years ago by
benformatics
3.9k • written 2.8 years ago by
scipio04
• 0
2
votes
14
replies
4.0k
views
QQ plots for eqtl data
MatrixEQTL
eqtl
updated 4.1 years ago by
Biostar
20 • written 6.1 years ago by
jamespower
▴ 100
0
votes
14
replies
2.2k
views
Bioinformatics tutoring
differentially
genes
expressed
microarray
updated 2.6 years ago by
Michael
54k • written 2.6 years ago by
bioinformatics
▴ 40
0
votes
14
replies
3.2k
views
FastQC reults /probloms in loading
RNA-Seq
7.5 years ago by
Arash
▴ 30
2
votes
14
replies
2.3k
views
How to map by bwa with 50 mismatches?
bwa
7.6 years ago by
agata88
▴ 870
1
vote
14
replies
600
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
6 hours ago by
hophuquy0944
• 0
8
votes
14
replies
2.6k
views
RNA-Seq analysis with standard p-value
RNA-Seq
7.3 years ago by
####
▴ 220
3
votes
14
replies
4.0k
views
TopHat Error Qual length differs from seq length
RNA-Seq
Assembly
software error
alignment
updated 5.7 years ago by
h.mon
35k • written 6.5 years ago by
williamsbrian5064
▴ 520
2
votes
14
replies
1.6k
views
VCF2MAF structural variant file issue.
VCF2MAF
updated 9 months ago by
Ram
43k • written 9 months ago by
The_PyPanda
▴ 10
0
votes
14
replies
785
views
frma normalization
affybatch
frma
mcp-counter
3 months ago by
michelafrancesconi9
▴ 20
9
votes
14
replies
4.4k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
hothriananya
▴ 70
3
votes
14
replies
1.3k
views
How to extract specific region from multiple bam files and merge the outputs into single bam?
bam
rna-seq
updated 6 months ago by
GenoMax
142k • written 6 months ago by
Vasu
▴ 770
1
vote
14
replies
3.4k
views
How to convert Haplotypes file to PLINK format data
R
plink
updated 11 months ago by
Ram
43k • written 6.0 years ago by
bha
▴ 80
1,000 results • Page
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Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
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Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
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