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1,000 results • Page
2 of 20
Sort: replies
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Views
Votes
Replies
4
votes
20
replies
1.3k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
3.4 years ago by
schlogl
▴ 150
9
votes
20
replies
3.4k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 11 weeks ago by
Ram
39k • written 4.8 years ago by
marongiu.luigi
▴ 680
6
votes
20
replies
5.6k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.0 years ago by
princy149
▴ 80
8
votes
20
replies
2.3k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
5.4 years ago by
corend
▴ 70
8
votes
20
replies
1.9k
views
Getting read depth for normal and tumour
R
WGS
vcf
4.2 years ago by
fi1d18
★ 4.2k
5
votes
20
replies
3.3k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 8 months ago by
Ram
39k • written 7.8 years ago by
Hans
▴ 130
5
votes
20
replies
7.4k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
6.8 years ago by
varsha619
▴ 90
8
votes
20
replies
1.9k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 12 months ago by
Ram
39k • written 4.9 years ago by
Bara'a
▴ 270
6
votes
19
replies
2.3k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
3.9 years ago by
aloke205
▴ 40
0
votes
19
replies
1.1k
views
map fasts files
RNA-Seq
FASTQ
R
5.3 years ago by
Learner
▴ 260
4
votes
19
replies
2.5k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
cool.abbecker
▴ 30
0
votes
19
replies
1.1k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
3.5 years ago by
marongiu.luigi
▴ 680
7
votes
19
replies
6.4k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 16 months ago by
Ram
39k • written 8.6 years ago by
mheiser1
▴ 10
1
vote
19
replies
5.9k
views
Conda install package - different internals
R
software error
updated 3.8 years ago by
Biostar
20 • written 3.8 years ago by
lihe.liu
▴ 30
1
vote
19
replies
1.6k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
4.5 years ago by
eozcan
▴ 10
0
votes
19
replies
8.3k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.0 years ago by
seta
★ 1.8k
17
votes
19
replies
2.2k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
6.8 years ago by
Gian77
▴ 60
0
votes
19
replies
3.3k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
5.4 years ago by
jaqx008
▴ 110
18
votes
19
replies
1.7k
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 6 months ago by
Ram
39k • written 4.4 years ago by
rbkh09
• 0
15
votes
19
replies
1.4k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.1 years ago by
Ram
39k • written 5.1 years ago by
Nadin.asal
• 0
3
votes
19
replies
4.9k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 4.1 years ago by
finswimmer
16k • written 4.1 years ago by
sruthi
▴ 40
22
votes
19
replies
2.5k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
6.7 years ago by
fi1d18
★ 4.2k
6
votes
19
replies
1.3k
views
Fastq header modification
sequence
next-gen
updated 5.2 years ago by
Ram
39k • written 5.2 years ago by
Guillaume
• 0
7
votes
19
replies
2.4k
views
mapping script process sleeping on server.
alignment
updated 13 months ago by
Ram
39k • written 8.3 years ago by
lvogel
▴ 30
0
votes
19
replies
1.2k
views
scatterplot in R
microarray
expression
gene
updated 8 months ago by
Ram
39k • written 8 months ago by
bioinformatics
▴ 10
9
votes
19
replies
1.7k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.4 years ago by
schlogl
▴ 150
0
votes
19
replies
2.2k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
22 months ago by
rheab1230
▴ 140
5
votes
19
replies
1.3k
views
how I can come up with a permanent error
R
software error
6.1 years ago by
fi1d18
★ 4.2k
13
votes
19
replies
4.5k
views
bbmerge not joining paired-end reads
bbmerge
alignment
5.5 years ago by
bioplanet
▴ 60
10
votes
19
replies
2.6k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.1 years ago by
GenoMax
130k • written 2.1 years ago by
matt
▴ 20
2
votes
18
replies
5.3k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
6.6 years ago by
Sumit Paliwal
▴ 40
2
votes
18
replies
1.8k
views
I need help in this
gene
weblems
alignment
updated 10 months ago by
Ram
39k • written 7.5 years ago by
efosa15
• 0
16
votes
18
replies
4.2k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.8 years ago by
Mensur Dlakic
★ 23k • written 3.8 years ago by
tikshyadav19
• 0
3
votes
18
replies
2.1k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 23 months ago by
Ram
39k • written 23 months ago by
Nai
▴ 50
2
votes
18
replies
1.9k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
17 months ago by
shivangi.agarwal800
▴ 120
7
votes
18
replies
4.1k
views
Fold change UP and Down in dplyr calculation
R
5.8 years ago by
1769mkc
★ 1.1k
4
votes
18
replies
3.4k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 10 months ago by
Ram
39k • written 7.5 years ago by
Joel TM
▴ 60
14
votes
18
replies
4.2k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
plink_9857
▴ 50
4
votes
18
replies
12k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 2.6 years ago by
Biostar
20 • written 4.8 years ago by
Shelle
▴ 30
0
votes
18
replies
1.3k
views
freebayes error variant calling
snp
2.8 years ago by
evelyn
▴ 220
4
votes
18
replies
2.6k
views
Inline barcodes in the reverse reads
barcodes
6.6 years ago by
Picasa
▴ 640
3
votes
18
replies
1.1k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
7 months ago by
lacb
▴ 120
7
votes
18
replies
4.0k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
6.6 years ago by
valerie
▴ 100
1
vote
18
replies
1.2k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 3.8 years ago by
Biostar
20 • written 3.8 years ago by
Natasha
▴ 40
0
votes
18
replies
1.0k
views
No gene name after annovar vcf file processing
vcf
annovar
3.6 years ago by
valerie
▴ 100
1
vote
18
replies
2.2k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
6.8 years ago by
Tom
▴ 40
7
votes
18
replies
7.7k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 16 months ago by
Ram
39k • written 8.6 years ago by
hana
▴ 190
5
votes
18
replies
5.3k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
3.5 years ago by
michelle.piquet
▴ 60
20
votes
17
replies
5.2k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
5.8 years ago by
Anand Rao
▴ 560
0
votes
17
replies
1.1k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
2.7 years ago by
Dunois
★ 2.3k
1,000 results • Page
2 of 20
Recent Votes
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
A: Finding zebrafish promoters ENSEMBL
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Comment: pal2nal -nogap -nomismatch options not working
by
Marie
• 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag
by
Pierre Lindenbaum
154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Ram
39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag
by
Ram
39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Arup Ghosh
3.2k
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