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918 results • Page
2 of 19
Sort: replies
Rank
Views
Votes
Replies
3
votes
11
replies
453
views
prefix extraction and preparation for mapping and variant calling
bash
updated 14 hours ago by
GenoMax
127k • written 4 days ago by
Human
• 0
1
vote
11
replies
1.5k
views
Extract information from gtf file
GTF
updated 4 days ago by
Ram
38k • written 13 months ago by
Human
• 0
7
votes
11
replies
1.4k
views
6 follow
how to convert to computational biology from bioinformatics
software
computational-biology
algorithm
updated 4 days ago by
Ram
38k • written 21 months ago by
biohubx
• 0
5
votes
11
replies
5.8k
views
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
HuEx-1_0-st
R
updated 1 day ago by
Ram
38k • written 5.0 years ago by
vinnu260
▴ 20
10
votes
11
replies
3.2k
views
Forum:
48 Replicate RNA-Seq Study Points to Replicates Needed for DGE
RNA-seq
differential-gene-expression
updated 10 hours ago by
Ram
38k • written 7.9 years ago by
support
▴ 640
1
vote
11
replies
1.1k
views
Bacterial RNAseq - Help for beginner
next-gen
RNA-Seq
Bacteria
updated 14 hours ago by
Ram
38k • written 2.9 years ago by
liz.marjory
▴ 10
11
votes
11
replies
1.4k
views
read.table function loss of columns in bed file
R
updated 4 days ago by
Ram
38k • written 6.0 years ago by
lauren.fehrman
• 0
6
votes
11
replies
681
views
Calculate RPKM
RPKM
1 day ago by
Chris
▴ 70
4
votes
11
replies
1.6k
views
Use BLAST Command Line Applications on combined FASTA files
BLAST
updated 4 days ago by
Ram
38k • written 18 months ago by
daver.v
▴ 30
3
votes
10
replies
7.6k
views
UCSC genes annotation of long non-coding RNAs in human
UCSC
lncRNAs
annotation
RNA-Seq
updated 4 days ago by
Ram
38k • written 8.8 years ago by
sasa_k
▴ 10
4
votes
10
replies
1.3k
views
bash script for merging R1 and R2 reads
fastq
bash
illumina
updated 4 days ago by
Ram
38k • written 9 months ago by
ieie
▴ 10
3
votes
10
replies
2.1k
views
Rosetta make_fragments.pl fails: "Cannot initialize readdb for nr database"
software-error
nr
rosetta
updated 4 days ago by
Ram
38k • written 2.9 years ago by
Alex_I
• 0
2
votes
10
replies
1.2k
views
multiple FASTA sequnces in to one full sequnce according to their chromosome number
NGS
FASTA
bam
updated 4 days ago by
Ram
38k • written 4.0 years ago by
Anu
• 0
0
votes
10
replies
2.8k
views
Difficulty using SPAdes - Error relating to access and specificity
SPAdes
software
De-novo
Assembler
updated 4 days ago by
Ram
38k • written 6.0 years ago by
gfrsims
• 0
6
votes
10
replies
2.5k
views
Genome assembly with RNA-seq data?
Assembly
genome
RNA-Seq
updated 14 hours ago by
Ram
38k • written 6.6 years ago by
Buffo
★ 2.0k
8
votes
10
replies
5.1k
views
gene filtering for agilent microarray using Limma
agilent microarray
limma
gene filtering
R
updated 16 hours ago by
Di Wu
• 0 • written 7.6 years ago by
rohit
▴ 60
2
votes
10
replies
5.9k
views
fq.gz file use
BioEdit
R
updated 4 days ago by
Ram
38k • written 4.0 years ago by
choi.yisoo.hi
• 0
3
votes
10
replies
2.0k
views
8 follow
ADMIXTURE Segmentatio fault
admixture
plink
vcf
updated 2 days ago by
1130291485
• 0 • written 21 months ago by
pmc.sa
▴ 40
4
votes
10
replies
2.8k
views
how to use the samtools filtering expression ?
samtools
updated 4 days ago by
Ram
38k • written 22 months ago by
Hippolyte
• 0
7
votes
10
replies
1.1k
views
col as names [solved]
R
updated 4 days ago by
Ram
38k • written 4.0 years ago by
demoraesdiogo2017
▴ 90
0
votes
10
replies
6.6k
views
Error: reads file does not look like a fastq file
fastq
bowtie2
ChIP-Seq
updated 4 days ago by
Ram
38k • written 6.5 years ago by
addilynn.beach
▴ 40
5
votes
10
replies
1.7k
views
Is it possible to count lines of fastq.gz file in R ?
fastq
R
updated 4 days ago by
Ram
38k • written 18 months ago by
br0104
• 0
3
votes
10
replies
2.2k
views
CellRanger scRNA .mtx only uses 15% of reads in .bam?
cellranger
single-cell
bam
mtx
scRNA
updated 4 days ago by
Ram
38k • written 3.0 years ago by
Diedes
▴ 20
11
votes
10
replies
8.7k
views
Select sequences from fastq.gz file
fastq
random-selection
updated 4 days ago by
Ram
38k • written 8.3 years ago by
msameet
▴ 50
11
votes
10
replies
3.3k
views
Forum:
Thinking of going into Bioinformatics
career
updated 4 days ago by
Ram
38k • written 6.4 years ago by
Eeyore88
▴ 40
2
votes
9
replies
466
views
Split fastq.gz file
fastq
updated 4 days ago by
Ram
38k • written 5 months ago by
sandy
• 0
8
votes
9
replies
633
views
Ribo-Seq Analysis
ribo-seq
ribosome
profiling
6 days ago by
phoenix.sum13
▴ 60
1
vote
9
replies
2.6k
views
bam to fasta error using samtools
fasta
bam
updated 4 days ago by
Ram
38k • written 6.0 years ago by
christacaggiano
▴ 60
8
votes
9
replies
2.3k
views
Forum:
Suggestions for small tools to add to Galaxy
Galaxy
updated 12 hours ago by
Ram
38k • written 7.9 years ago by
Devon Ryan
103k
1
vote
9
replies
2.6k
views
convert csv file to bed file
bed
updated 8 hours ago by
Ram
38k • written 13 months ago by
oldtownroald
• 0
4
votes
9
replies
534
views
Downloading NCBI Blast nt database
nucleotide
blast
nt
genomics
database
updated 5 days ago by
size_t
▴ 60 • written 5 days ago by
rgray
• 0
3
votes
9
replies
5.8k
views
bcftools doesn't normalize the vcf file
vcf
bcftools
normalize
updated 1 day ago by
Ram
38k • written 4.2 years ago by
seta
★ 1.8k
2
votes
9
replies
375
views
STARsolo
STARsolo
scRNAseq
updated 5 days ago by
GenoMax
127k • written 5 days ago by
No.Lar037477
▴ 10
11
votes
9
replies
6.4k
views
Extracting certain columns from VCF file
vcf
genotype
vcftools
exome
updated 4 days ago by
Ram
38k • written 4.8 years ago by
gradstudentNew
▴ 50
2
votes
9
replies
680
views
Padj Values Problem For Multiple Samples in DESeq2
sequencing
RNA-seq
R
updated 4 days ago by
Ram
38k • written 2.1 years ago by
Aynur
▴ 50
8
votes
9
replies
2.6k
views
Sample .sam file
next-gen
sam
alignment
sequence
updated 4 days ago by
Ram
38k • written 6.6 years ago by
torkel.loman
• 0
5
votes
9
replies
1.9k
views
Program to find genes up/down-regulated by a given gene
geo
upregulated
gene
downregulated
updated 5 days ago by
Ram
38k • written 8.1 years ago by
c_u
▴ 500
1
vote
9
replies
2.8k
views
6 follow
Somatic variant call
Mutect2
Varscan
variant-filtering
SNP
updated 1 day ago by
Ram
38k • written 5.9 years ago by
sktbanerjee1
▴ 30
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 1 day ago by
Ram
38k • written 7.9 years ago by
gaurav.singh
▴ 10
1
vote
8
replies
1.2k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq
pySCENIC
loom
updated 10 hours ago by
Ram
38k • written 7 months ago by
Jacob
• 0
7
votes
8
replies
452
views
How do you obtain a list of transcription factors from a genome?
transcription-factor
updated 4 days ago by
Ram
38k • written 5 months ago by
DNAngel
▴ 240
10
votes
8
replies
2.5k
views
Visualization of maf alignments in JBrowse
maf
conservation
Multiz-Alignments
updated 4 days ago by
Ram
38k • written 6.9 years ago by
ifreecell
▴ 220
11
votes
8
replies
479
views
Sorting a STAR-output bam file with samtools leads to a significant reduction in size of the sorted bam file
samtools
STAR
3 days ago by
e.r.zakiev
▴ 30
1
vote
8
replies
1.9k
views
6 follow
DESeq2 count matrix read in
deseq2
R
updated 4 days ago by
Ram
38k • written 22 months ago by
Gregor Rot
▴ 540
4
votes
8
replies
1.1k
views
why those reads don't contain 0x2
bam
sam
updated 14 hours ago by
Ram
38k • written 17 months ago by
zt10122
▴ 20
6
votes
8
replies
311
views
6 follow
Snakemake vs Nextflow Upcoming bioinformatics Project
Programming
Masters
8 hours ago by
rackbersingh
• 0
3
votes
8
replies
5.8k
views
Help with designing limma contrast matrix
limma
software error
updated 2 days ago by
Kevin Blighe
84k • written 5.0 years ago by
fi1d18
★ 4.1k
4
votes
8
replies
2.3k
views
7 follow
Converting an output de-novo transcriptome assembled with Trinity to a .gff3 file
Trinity
updated 1 day ago by
Juke34
7.7k • written 3.5 years ago by
Raito92
▴ 80
2
votes
8
replies
2.0k
views
Sift on the VEP output
missense-variant
SIFT
SNP
VEP
updated 1 day ago by
Ram
38k • written 4.4 years ago by
mostafarafiepour
▴ 160
3
votes
8
replies
1.9k
views
7 follow
Forum:
Bioinfomatic course or training for Computer Science professional
Training
Courses
updated 13 hours ago by
Ram
38k • written 5.5 years ago by
kianc
• 0
918 results • Page
2 of 19
Recent Votes
Answer: RNA-SEQ
Comment: RNA-SEQ
Comment: RNA-SEQ
Answer: RNA-SEQ
Gene Set Enrichment Analysis
Can I sort my bam files with Picard MergeSamFiles?
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
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GenoMax
127k
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Recent Replies
Answer: activity of unloaded/unassembled Tn5
by
callumjcparr
• 0
So I hope someone is still interested in this. We have taken to preparing recombinant Tn5 now as it's much cheaper than commercial supp…
Comment: RNA-SEQ
by
ali
• 0
thanks for your helping
Comment: TSS of protein coding genes
by
ConvolutedGenome
▴ 10
I am quite confused with GENCODE GTF file, So, within the GENCODE GTF file, I noticed that each (protein-coding) gene has multiple "transc…
Comment: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da
by
iraun
5.8k
Hi! I personally use [SplAdder][1], in case you want to add it to your list :). [1]: https://github.com/ratschlab/spladder
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
by
Andy
• 0
Really the only needed, that help worked, thank's
Comment: Active enhancers for mm39
by
seidel
11k
Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…
Comment: Creating loop for read groups using Picard
by
ntsopoul
▴ 20
try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.
Comment: how to create interacting Hi-C peaks
by
rheab1230
▴ 140
Thank you. I will use this package since I am more familiar with R
Comment: how to create interacting Hi-C peaks
by
rheab1230
▴ 140
thank you. i will go through it
Comment: Fastqc report analysis
by
npavliukovec
• 0
Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…
Comment: My fastq files(paired end) have different read number
by
kimgeng
• 0
Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…
Answer: My fastq files(paired end) have different read number
by
ntsopoul
▴ 20
Yes, this is normal because depending on how you generate the bam file, the non-aligning reads are saved in the .bam file along the properl…
Answer: Can I use abundance from Tximport to compare the expression level of transcript
by
ntsopoul
▴ 20
No, you should not do that since the count matrix is not normalized. Also, the statistics for getting a pValue requires consideration of al…
Comment: Easy way to split VCF file by chromosome
by
Joana
• 0
You need to run bcftools index on your vcf file before running the suggested command.
Comment: Fastqc report analysis
by
ntsopoul
▴ 20
I think you are fine, no worries. Will you go ahead an align the fastq files to a genome? Do you know how?
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