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1,148 results • Page
1 of 23
Sort: Votes
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Views
Votes
Replies
276
votes
39
replies
164k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 1 day ago by
Ram
38k • written 8.6 years ago by
Obi Griffith
20k
251
votes
36
replies
30k
views
27 follow
Forum:
How Do You Manage Your Files & Directories For Your Projects ?
project-management
file-management
updated 2 days ago by
Ram
38k • written 12.9 years ago by
Pierre Lindenbaum
153k
130
votes
123
replies
28k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 3 days ago by
krushnach80
★ 1.1k • written 4.4 years ago by
Kevin Blighe
84k
100
votes
36
replies
27k
views
33 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 3 days ago by
Simon
▴ 20 • written 9.4 years ago by
14134125465346445
★ 3.6k
75
votes
22
replies
49k
views
17 follow
How To Download All Sra Samples At Once ?
geo
sra
updated 2 days ago by
Ram
38k • written 9.1 years ago by
biorepine
★ 1.5k
58
votes
23
replies
12k
views
11 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 2 days ago by
Ram
38k • written 4.1 years ago by
Phil Ewels
★ 1.1k
47
votes
4
replies
9.8k
views
How do experienced people look for full reference genomes?
reference-genome
fasta
updated 1 day ago by
Ram
38k • written 8.8 years ago by
John Smith
▴ 320
42
votes
19
replies
5.9k
views
7 follow
Makefile-Driven Workflows And Bioconductor Objects
r
bioconductor
workflow
pipeline
updated 3 days ago by
Ram
38k • written 10.1 years ago by
gbayon
▴ 170
34
votes
30
replies
1.8k
views
6 follow
Tool:
BioFlows - Container-enabled Bioinformatics pipeline engine
workflow
next-gen
RNA-Seq
pipeline
updated 4 days ago by
Ram
38k • written 2.3 years ago by
mfawzy.sami
▴ 90
32
votes
5
replies
5.2k
views
Forum:
ipython notebooks on bioinformatics and genomics
python
updated 3 days ago by
Ram
38k • written 7.7 years ago by
Pappu
★ 2.1k
29
votes
14
replies
7.9k
views
7 follow
How To Download All The Introns From Ensembl
ensembl
fasta
intron
updated 1 day ago by
Ram
38k • written 11.6 years ago by
Anima Mundi
★ 2.9k
27
votes
19
replies
3.8k
views
10 follow
Forum:
Google genomics cloud platform ?
genome
cloud
updated 4 days ago by
Ram
38k • written 7.8 years ago by
GouthamAtla
12k
26
votes
4
replies
7.6k
views
How To Download All The Introns From Ucsc
fasta
intron
assembly
ucsc
updated 1 day ago by
Ram
38k • written 11.2 years ago by
Anima Mundi
★ 2.9k
25
votes
13
replies
25k
views
8 follow
Bowtie2 parameters for best alignment
alignment
Assembly
genome
SNP
updated 5 days ago by
Medhat
9.5k • written 8.8 years ago by
cvu
▴ 180
23
votes
14
replies
3.5k
views
7 follow
Which Of The 2011 Nar Database Submissions Are Fully Accessible?
web-service
updated 1 day ago by
Ram
38k • written 12.2 years ago by
Jeremy Leipzig
21k
21
votes
23
replies
2.8k
views
7 follow
Very low mapping rate of a bam file, reasons?
next-gen
alignment
bam
updated 3 days ago by
Ram
38k • written 6.9 years ago by
nidoo.beg
▴ 20
20
votes
13
replies
2.8k
views
Download Genomic Ranges From A List Of Coordinates Via Web
fasta
coordinates
updated 1 day ago by
Ram
38k • written 11.2 years ago by
Anima Mundi
★ 2.9k
20
votes
12
replies
4.5k
views
7 follow
Simple Fasta Parsing Is Not Simple.
fasta
python
biopython
updated 2 days ago by
Ram
38k • written 12.9 years ago by
Vlinxify
▴ 120
19
votes
11
replies
18k
views
How to transpose large amounts of datasets in excel
Transpose
excel
updated 1 day ago by
Ram
38k • written 7.7 years ago by
Vanceed
▴ 30
18
votes
27
replies
17k
views
20 follow
Where Can I Download Vcf Files For Publicly Available Data?
vcf
snp
updated 1 day ago by
Ram
38k • written 11.3 years ago by
Kevin
▴ 640
17
votes
18
replies
16k
views
How to download the complete database Nucleotide collection (nr/nt)?
blast
nr
nt
updated 1 day ago by
Ram
38k • written 3.7 years ago by
marongiu.luigi
▴ 670
17
votes
26
replies
1.4k
views
File conversion in bash, discrepancy in number of lines after conversion.
bash
updated 3 days ago by
Ram
38k • written 2.9 years ago by
ATCG
▴ 380
17
votes
29
replies
5.6k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff
parse
updated 3 days ago by
Juke34
7.7k • written 4.5 years ago by
a.rex
▴ 350
17
votes
8
replies
468
views
Where do find virulence gene information in a gff/gtf file?
microbial
genomics
gff
annotation
gtf
3 days ago by
sovrappensiero
▴ 90
16
votes
10
replies
12k
views
6 follow
Where Can I Download All Exons Of The Human Genome In Fasta Format (One Big File!) ?
fasta
human-genome
exon
updated 1 day ago by
Ram
38k • written 10.0 years ago by
mariusorion
▴ 60
16
votes
5
replies
11k
views
Phylip To Newick Format Conversion!
phylip
newick
python
updated 2 days ago by
Ram
38k • written 12.9 years ago by
Thaman
★ 3.3k
16
votes
19
replies
2.3k
views
7 follow
difficulty in underestanding terms and graphs
RNA-Seq
updated 4 days ago by
Ram
38k • written 6.8 years ago by
DavidP
▴ 60
15
votes
7
replies
10k
views
Refseq Proteins For A Given Taxid
protein
biopython
refseq
updated 1 day ago by
Ram
38k • written 11.1 years ago by
Chris
★ 1.6k
14
votes
8
replies
6.8k
views
6 follow
Split Fastq File Into Different Files Only Comprising One Chromosome Each
fastq
updated 2 days ago by
Ram
38k • written 12.3 years ago by
Smitz
▴ 50
14
votes
13
replies
4.5k
views
Parsing Custom Snp Info File In Python
python
updated 2 days ago by
Ram
38k • written 12.8 years ago by
Eric Normandeau
11k
14
votes
15
replies
2.1k
views
fastq parsing inefficiencies with python
python
RNA-Seq
updated 3 days ago by
Ram
38k • written 5.1 years ago by
brismiller
▴ 50
13
votes
9
replies
22k
views
6 follow
How To Download Full Genome Sequence
genome
sequence
updated 1 day ago by
Ram
38k • written 11.8 years ago by
Palu
▴ 240
13
votes
4
replies
8.1k
views
Downloading Fasta Files
fasta
blast
genome
sequence
updated 1 day ago by
Ram
38k • written 12.4 years ago by
Mcdenzlix
▴ 50
13
votes
3
replies
33k
views
Drawing venn diagram in R
ChIP-Seq
venn-diagram
updated 4 days ago by
Ram
38k • written 7.9 years ago by
Rashedul Islam
▴ 450
13
votes
11
replies
4.3k
views
TCGA immunotherapy treated melanoma data
mutation
tcga
SNP
updated 1 day ago by
Ram
38k • written 4.5 years ago by
Pin.Bioinf
▴ 330
13
votes
41
replies
1.5k
views
Is my file created completely
sam
BWA-MEM
BWA
updated 3 days ago by
Ram
38k • written 5.9 years ago by
micro32uvas
▴ 10
12
votes
14
replies
4.2k
views
7 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 3 days ago by
Damianos P. Melidis
▴ 40 • written 2.8 years ago by
Eugene A
▴ 170
12
votes
4
replies
6.5k
views
Help With Downloading Sequences From Ensembl
ensembl
perl
sequence
updated 1 day ago by
Ram
38k • written 12.6 years ago by
Sashi Kiran Challa
▴ 310
12
votes
20
replies
3.0k
views
7 follow
How to write out a ID and AA sequence from a SWISS PROT database file into a new file in a specific order using python?
protein
python
updated 3 days ago by
Ram
38k • written 15 months ago by
M.O.L.S
▴ 100
12
votes
20
replies
2.6k
views
Forum:
Starting a career in Bioinformatics
career
updated 4 days ago by
Ram
38k • written 6.8 years ago by
rupashree.choudhury
▴ 10
12
votes
4
replies
4.0k
views
Retrieve genbank viral genomes
ncbi
genbank
viral-genome
updated 1 day ago by
Ram
38k • written 5.7 years ago by
erwan.scaon
▴ 910
12
votes
9
replies
9.0k
views
6 follow
How to download genome assemblies from NCBI with a list of GCA identifiers?
ncbi
Assembly
updated 1 day ago by
Ram
38k • written 4.4 years ago by
O.rka
▴ 650
12
votes
7
replies
3.0k
views
Forum:
Which is better for job opportunities: Metagenomics OR Plant biotechnology
Metagenomics
Plant-biotechnology
career
updated 5 days ago by
Ram
38k • written 8.0 years ago by
anokimchen
• 0
12
votes
4
replies
1.8k
views
Tutorial:
Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR
DESeq2
updated 2 days ago by
Ram
38k • written 5.5 years ago by
KVC_bioinfo
▴ 570
12
votes
4
replies
15k
views
Command to extract SNPs from VCF file using bcftool
SNPs
bcftools
VCF
updated 5 days ago by
Ram
38k • written 6.9 years ago by
MAPK
★ 2.0k
12
votes
4
replies
4.1k
views
Quantile (Limma-voom) normalization
RNA-Seq
voom
updated 2 days ago by
Ram
38k • written 5.5 years ago by
KVC_bioinfo
▴ 570
12
votes
9
replies
5.8k
views
9 follow
Forum:
Bioinformatics and wet lab science combined
career
updated 1 day ago by
Ram
38k • written 7.7 years ago by
tretyacv
▴ 40
11
votes
1
reply
3.3k
views
How to download a whole ICGC release of processed data?
icgc
updated 1 day ago by
Ram
38k • written 6.2 years ago by
Michael Schubert
★ 7.1k
11
votes
8
replies
2.0k
views
Download Brachypodium Distachyon Genome
genome
updated 1 day ago by
Ram
38k • written 11.7 years ago by
Sara
▴ 130
11
votes
6
replies
5.5k
views
Where Can I Download Nucleotide Sequences Of Bacterial Genes?
bacteria
gene
updated 1 day ago by
Ram
38k • written 11.1 years ago by
Tianyang Li
▴ 500
1,148 results • Page
1 of 23
Recent Votes
downloading human gene symbol with duplicates
Getting a list of protein coding genes in human
Answer: How to make cut off linein cluster,
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NCBI's IgBLAST version 1.21.0 is now available
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prabin.dm
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Recent Replies
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
Adaline.D
• 0
That explains a lot to me. Thank you, seidel! They used Affymetrix Human Gene 1.0 ST Array chips. Hope you have a wonderful day.
Comment: How to make cut off linein cluster,
by
Info.shi
▴ 20
Thank you so much it worked. I highly appreciate your help.
Answer: How to make cut off linein cluster,
by
Jeremy
▴ 770
Try adding the following line of code: abline(h = .02)
Comment: Problem with fatsq-dump
by
Utpal
• 0
Thank you for your support. I tried the command conda install -c bioconda sra-tools But, still with the command, fastq-dump it return…
Comment: RNA Sequencing and Vg pan -transcriptome build
by
Jordan M Eizenga
▴ 70
The `vg mpmap` subcommand has features for mapping RNA-seq data to a graph. We describe in more detail in [this publication][1], including …
Comment: how to import hdf5 Hi-C data into R using HiTC package
by
rpolicastro
11k
From the error you may need to specify the file path instead of passing it the imported data.
Comment: RNA Sequencing and Vg pan -transcriptome build
by
cmdcolin
★ 2.9k
i am not sure how about the data input format but 'hisat2' is able to 'align rna-seq to a population reference'. this may be a little diffe…
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
seidel
11k
What technology is the GEO data set derived from? Signal intensity implies a fluorescence read out (i.e. microarray). If that's the case, y…
Comment: Log2 FC Threshold
by
seidel
11k
Given that 0.2 is a 1.15 fold change (2^0.2) you're right to be skeptical, but there's no clear answer as to the significance. Consider tha…
Comment: Read lengths greater than insert length
by
GenoMax
127k
As I said above the adapters are each ~60 bp long so they add ~120 bp (5' and 3' end adapters) to the length of the DNA fragment. What you …
Comment: Problem with fatsq-dump
by
GenoMax
127k
Looks like the developers have an answer for this error: https://github.com/ncbi/sra-tools/issues/139 At least the program seems to be ins…
Comment: Read lengths greater than insert length
by
shpak.max
▴ 30
I'm not claiming that all fragment lengths are exactly 50, the typical range for my data is 45-60. However, my read lengths are all 150, so…
Answer: Read lengths greater than insert length
by
GenoMax
127k
Illumina libraries are made by adding adapters to the ends of DNA fragment(s). Those adapters themselves are about 60 nucleotides long. Not…
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang
by
Rob
5.9k
If you have the raw data, you can easily get this information using [alevin-fry](https://www.nature.com/articles/s41592-022-01408-3). It pr…
Answer: Matching gene-expression data with clinical data: best practices.
by
pilargmarch
▴ 60
I really like using [the R/Bioconductor package TCGAbiolinks][1], it gives you clinical and expression data by patient ID. [1]: http…
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