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1,145 results • Page 1 of 23
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130
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123
replies
28k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 3 days ago by ★ 1.1k • written 4.4 years ago by 84k
118
votes
53
replies
87k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 6 days ago by • 0 • written 8.8 years ago by ▴ 330
13
votes
41
replies
1.5k
views
Is my file created completely
sam BWA-MEM BWA
updated 2 days ago by 38k • written 5.9 years ago by ▴ 10
276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 16 hours ago by 38k • written 8.6 years ago by 20k
100
votes
36
replies
27k
views
33 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 2 days ago by ▴ 20 • written 9.4 years ago by ★ 3.6k
251
votes
36
replies
30k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
project-management file-management
updated 1 day ago by 38k • written 12.9 years ago by 153k
34
votes
30
replies
1.8k
views
6 follow
Tool: BioFlows - Container-enabled Bioinformatics pipeline engine
workflow next-gen RNA-Seq pipeline
updated 3 days ago by 38k • written 2.3 years ago by ▴ 90
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 2 days ago by 7.7k • written 4.5 years ago by ▴ 350
18
votes
27
replies
17k
views
20 follow
Where Can I Download Vcf Files For Publicly Available Data?
vcf snp
updated 15 hours ago by 38k • written 11.3 years ago by ▴ 640
6
votes
26
replies
7.5k
views
Realign BAM files to other reference file
bam samtools
updated 2 days ago by 38k • written 4.7 years ago by ▴ 670
17
votes
26
replies
1.4k
views
File conversion in bash, discrepancy in number of lines after conversion.
bash
updated 2 days ago by 38k • written 2.9 years ago by ▴ 380
8
votes
25
replies
1.9k
views
construction of a database
sql noSQL neo4j database
updated 3 days ago by 38k • written 22 months ago by ▴ 20
21
votes
23
replies
2.8k
views
7 follow
Very low mapping rate of a bam file, reasons?
next-gen alignment bam
updated 2 days ago by 38k • written 6.9 years ago by ▴ 20
5
votes
23
replies
2.1k
views
Please help with connecting the part of the header in a fasta file with another text file
programming fasta
updated 2 days ago by 38k • written 6.7 years ago by ★ 1.8k
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 1 day ago by 38k • written 4.1 years ago by ★ 1.1k
6
votes
22
replies
24k
views
12 follow
CluserProfiler message "No gene can be mapped"
R
updated 3 days ago by • 0 • written 5.0 years ago by ▴ 130
10
votes
22
replies
6.0k
views
12 follow
Easy way to split VCF file by chromosome
sequence TOPMED chromosome Imputation SNP
updated 2 days ago by 38k • written 14 months ago by ▴ 10
75
votes
22
replies
49k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 1 day ago by 38k • written 9.1 years ago by ★ 1.5k
6
votes
20
replies
2.6k
views
problem with vcf file
vcf linux SNP
updated 2 days ago by 38k • written 6.0 years ago by ▴ 40
7
votes
20
replies
1.9k
views
NcbiblastpCommandline alignment results are different from blast webpage
alignment biopython blastp
updated 4 days ago by 38k • written 11 months ago by • 0
12
votes
20
replies
2.6k
views
Forum: Starting a career in Bioinformatics
career
updated 3 days ago by 38k • written 6.8 years ago by ▴ 10
0
votes
20
replies
2.6k
views
Plink 2 user error converting .bgen to bcf
bcf Plink bgen2
updated 4 days ago by 38k • written 14 months ago by • 0
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard SAM
updated 2 days ago by 38k • written 4.6 years ago by ▴ 670
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 2 days ago by 38k • written 15 months ago by ▴ 100
27
votes
19
replies
3.8k
views
10 follow
Forum: Google genomics cloud platform ?
genome cloud
updated 3 days ago by 38k • written 7.8 years ago by 12k
42
votes
19
replies
5.9k
views
7 follow
Makefile-Driven Workflows And Bioconductor Objects
r bioconductor workflow pipeline
updated 2 days ago by 38k • written 10.1 years ago by ▴ 170
16
votes
19
replies
2.3k
views
7 follow
difficulty in underestanding terms and graphs
RNA-Seq
updated 3 days ago by 38k • written 6.8 years ago by ▴ 60
17
votes
18
replies
16k
views
How to download the complete database Nucleotide collection (nr/nt)?
blast nr nt
updated 16 hours ago by 38k • written 3.7 years ago by ▴ 670
4
votes
18
replies
2.7k
views
unimplemented type 'list' in 'EncodeElement' error in a Rscript run in Ubuntu terminal
Rscript JUM write.table
21 hours ago by farzaneafzali ▴ 70
7
votes
18
replies
17k
views
How to check if there is any extra space or blank line in the fasta file?
fasta
updated 2 days ago by 38k • written 7.2 years ago by ★ 1.8k
10
votes
18
replies
14k
views
8 follow
Please help with removing spaces from fasta file
fasta
updated 2 days ago by 38k • written 7.2 years ago by ★ 1.8k
4
votes
17
replies
2.4k
views
Selecting intergenic regions
grep shell
updated 2 days ago by 38k • written 4.8 years ago by ▴ 220
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 2 days ago by 38k • written 4.6 years ago by ▴ 670
0
votes
16
replies
1.4k
views
How to convert ncbi gff file to ensembl gff format
bcftools gff
updated 3 days ago by 38k • written 7 months ago by ▴ 10
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta vcf genbank gff
updated 2 days ago by 38k • written 4.5 years ago by ▴ 670
1
vote
15
replies
1.2k
views
Samtools merge Illumina and PB bam file empty
Illumina samtools Bam PacBio
updated 2 days ago by 38k • written 2.6 years ago by • 0
14
votes
15
replies
2.1k
views
fastq parsing inefficiencies with python
python RNA-Seq
updated 2 days ago by 38k • written 5.1 years ago by ▴ 50
9
votes
14
replies
1.0k
views
6 follow
Downloading a huge amount of Fastq files
fastq
updated 1 day ago by 38k • written 8 months ago by ▴ 50
23
votes
14
replies
3.5k
views
7 follow
Which Of The 2011 Nar Database Submissions Are Fully Accessible?
web-service
updated 14 hours ago by 38k • written 12.2 years ago by 21k
8
votes
14
replies
887
views
"transcript reads were aligned to the RefSeq transcriptome (downloaded March 2013) using Tophat" was done by orginal author.Please help me to get tha…
RNA-Seq RefSeq
updated 1 day ago by 38k • written 12 months ago by • 0
12
votes
14
replies
4.2k
views
7 follow
ACMG assignment tools
wes acmg WES WGS
updated 3 days ago by ▴ 40 • written 2.8 years ago by ▴ 170
29
votes
14
replies
7.9k
views
7 follow
How To Download All The Introns From Ensembl
ensembl fasta intron
updated 14 hours ago by 38k • written 11.6 years ago by ★ 2.9k
11
votes
13
replies
4.7k
views
6 follow
Rosalind exercise: Finding a Motif in DNA
python rosalind
updated 1 day ago by 38k • written 2.7 years ago by ▴ 20
20
votes
13
replies
2.8k
views
Download Genomic Ranges From A List Of Coordinates Via Web
fasta coordinates
updated 15 hours ago by 38k • written 11.1 years ago by ★ 2.9k
6
votes
13
replies
1.5k
views
10x 3' library creates R1 and R2 fastq files with the same read length
10x fastq scRNA-seq
updated 2 days ago by 127k • written 8 months ago by ▴ 370
1
vote
13
replies
4.5k
views
6 follow
/bin/bash/ command not found
snakePipes snakemake
updated 1 day ago by 38k • written 3.1 years ago by ▴ 60
25
votes
13
replies
25k
views
8 follow
Bowtie2 parameters for best alignment
alignment Assembly genome SNP
updated 4 days ago by 9.5k • written 8.8 years ago by ▴ 180
4
votes
13
replies
916
views
6 follow
select rows in a tab-delimited ed file
linux text
updated 3 days ago by 38k • written 8 months ago by ▴ 40
14
votes
13
replies
4.5k
views
Parsing Custom Snp Info File In Python
python
updated 1 day ago by 38k • written 12.8 years ago by 11k
0
votes
13
replies
2.3k
views
How to download all searched SRA result data at once?
sra data-mining
updated 15 hours ago by 38k • written 5.7 years ago by • 0
1,145 results • Page 1 of 23
Recent Votes
Difference between RNA-sq and Transcriptome
Rat lung transcriptome
A: microarray, RNAseq, CEL, edgeR, etc. for DGE analysis
Converting SNP from chr:pos to rs number using PLINK?
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
Answer: Cellranger sequencing
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
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Recent Replies
Answer: error in downloading of some accesions with fastq-dump by Utpal • 0
Hi, could you please let me know how to upgrade sratoolkit in centos? Thanks and regards,
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang by benformatics 3.5k
I don't think you can get that information specifically: https://kb.10xgenomics.com/hc/en-us/articles/360021902671-Can-we-detect-splice-va…
Answer: Problem with fatsq-dump by Utpal • 0
with the command which fastq-dump it returns: ~/.conda/envs/sratoolkit_env/bin/fastq-dump Thanks.
Comment: Remove part of headers in FASTA file by Pierre Lindenbaum 153k
Use `cut -d ' '`
Answer: Problem running interproscan-5.15-54.0 for protein sequences by Pratyay • 0
Hi, can you guide me how to compile the src folder? Many thanks!
Comment: Matching gene-expression data with clinical data: best practices. by krushnach80 ★ 1.1k
You can check [this][1] [1]: https://www.linkedomics.org/
Answer: Matching gene-expression data with clinical data: best practices. by jose.sgomez94 • 0
Figured out one can use the TCGAutils package in R and UUIDtobarcode() function. Still, suggestions of best practices would be awesome!
Answer: Understanding multifactor designs and control variables in DESeq2 by FrankStarling ▴ 50
https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2021/RNAseq/Markdowns/10_DE_analysis_with_DESeq2.Solutions.html …
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by Adaline.D • 0
I appreciate your help, LChart! I will use raw data in case of a substantial loss of power. (1) The publication did a PCA and then analy…
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by LChart 2.2k
Short answer: use LIMMA Long answer: edgeR uses a negative binomial model, and expects *counts* and not *values*. Please read section 2.8.…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Wayne, both of these methods work beautifully. I really appreciate the detail you provided, thank you so much for your help!
Comment: Ortholog assembly and extraction by dthorbur ▴ 420
I really like `orthofinder` and use it frequently, but there are also plenty of other tools out there. [Here](https://academic.oup.com/mbe/…
Comment: chloroplast genome gaps by ugur • 0
after alignment, it occurs in different sizes of gaps
Answer: Cellranger sequencing by ATpoint 70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
Answer: Assembly at lineage level from shotgun data ? by Mensur Dlakic ★ 23k
The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a referenc…
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