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781 results • Page 1 of 16
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226
votes
39
replies
276k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 3 days ago by 36k • written 12.8 years ago by ▴ 620
39
votes
38
replies
6.3k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 3 days ago by 36k • written 6.8 years ago by 13k
105
votes
26
replies
36k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 5 days ago by 36k • written 9.6 years ago by ▴ 810
18
votes
23
replies
3.7k
views
9 follow
Lack of consensus between NGS & Sanger sequencing on indels/mutations
Sanger NGS variant-calling BWA-MEM indel
updated 4 days ago by 36k • written 6.7 years ago by ▴ 270
37
votes
22
replies
19k
views
17 follow
Deconvolution Methods on RNA-Seq Data (Mixed cell types)
RNA-Seq deconvolution
updated 5 days ago by 36k • written 6.9 years ago by ▴ 140
74
votes
21
replies
10k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
updated 2 days ago by • 0 • written 22 months ago by ★ 2.6k
26
votes
21
replies
8.5k
views
13 follow
Tool for random access to indexed BAM files in S3?
cloud BAM
updated 4 days ago by 36k • written 7.1 years ago by ★ 1.6k
11
votes
20
replies
4.7k
views
9 follow
Extract sequences from a list of ID
software error sequence
updated 55 minutes ago by ▴ 20 • written 21 months ago by ▴ 30
1
vote
20
replies
6.7k
views
What is wrong here with bbmap and java
RNA-seq alignment java bbmap
updated 6 days ago by 36k • written 6.7 years ago by ★ 1.7k
8
votes
19
replies
4.3k
views
H3K4Me3 ChIP-Seq signal at promoter
H3K4Me3 ChIP-Seq
updated 6 days ago by 36k • written 6.7 years ago by ▴ 200
28
votes
19
replies
2.3k
views
9 follow
what is the biological replications
RNA-Seq next-gen
updated 6 days ago by 36k • written 6.7 years ago by ▴ 30
93
votes
19
replies
84k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 4 days ago by 36k • written 12.5 years ago by 27k
4
votes
18
replies
3.0k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq virus reads fusion
updated 6 days ago by 36k • written 6.7 years ago by ▴ 60
4
votes
18
replies
3.8k
views
7 follow
Aborted session in R using featureCounts in Rsubread
Rsubread featureCounts R BAM miRNA-Seq
updated 6 days ago by 36k • written 6.7 years ago by • 0
9
votes
18
replies
649
views
How to know the genome indices from STAR is correct
STAR
4 days ago by Chris • 0
42
votes
16
replies
20k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 6 days ago by 36k • written 6.9 years ago by ★ 2.3k
18
votes
16
replies
5.8k
views
8 follow
de novo sequence assembly with extremely high coverage
de-novo-sequence-assembly Illumina high-coverage
updated 5 days ago by 36k • written 6.7 years ago by ▴ 20
8
votes
15
replies
6.1k
views
6 follow
Beagle 4.1 error : Possible data conversion issue
VCF PLINK SNP BEAGLE
updated 4 days ago by 36k • written 6.7 years ago by ▴ 70
9
votes
15
replies
4.6k
views
Finding Chip Seq Overlaps with Bed files
bedops ChIP-Seq bedmap bedtools
updated 5 days ago by 36k • written 6.7 years ago by ▴ 540
10
votes
14
replies
572
views
7 follow
AF = 0.5 in chrX, VCF of a male
VCF AF chrX
4 days ago by paolo ▴ 10
10
votes
14
replies
14k
views
7 follow
Can't locate Bio/SeqIO.pm
AMPHORA Perl
updated 3 days ago by 36k • written 3.8 years ago by ▴ 10
0
votes
13
replies
2.0k
views
genes in gtf do not exist in the merged.gtf after cuffmerge
next-gen rna-seq alignment
updated 5 days ago by 36k • written 6.7 years ago by ▴ 110
2
votes
13
replies
6.0k
views
How to obtain TSS from list of given genes
RNA-Seq r
updated 5 days ago by 36k • written 6.7 years ago by ▴ 30
6
votes
13
replies
5.7k
views
DESeq2 and edgeR - no agreement between results
RNA-Seq edgeR DESeq2
updated 6 days ago by 36k • written 6.7 years ago by ▴ 60
5
votes
13
replies
381
views
Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
Institute ftp Broad gatk
3 days ago by appropiate ▴ 40
2
votes
12
replies
3.5k
views
cufflinks and average FPKM
RNA-Seq sequencing alignment
updated 5 days ago by 36k • written 6.7 years ago by ▴ 110
15
votes
12
replies
65k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast blastn sift makeblastdb
updated 2 days ago by • 0 • written 7.8 years ago by ▴ 310
5
votes
12
replies
443
views
SRA not splitting when trying to download fastq
SRA FASTQ Linux scRNA
updated 6 days ago by ▴ 280 • written 10 days ago by ▴ 20
5
votes
11
replies
4.7k
views
getting RPKM and VST using DEseq2 package
R RNA-Seq DEseq2
updated 1 day ago by 6.4k • written 6.8 years ago by ★ 4.1k
16
votes
11
replies
7.0k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation Tutorial
3 days ago by Ram 36k
2
votes
11
replies
8.8k
views
Regarding filter primary alignment
genome next-gen sequencing SNP
updated 2 days ago by • 0 • written 5.1 years ago by ▴ 40
33
votes
11
replies
7.2k
views
13 follow
Forum: Gallery: Computational tools for DNA methylation
computational-tools methylation
updated 6 days ago by 36k • written 6.8 years ago by ★ 9.1k
5
votes
11
replies
2.2k
views
What is the reason for deviation from diagonal?
snp genetics ggplot statistics
updated 5 days ago by 36k • written 6.7 years ago by ▴ 290
0
votes
11
replies
381
views
filtering multi sample vcf file
vcf filtering file
updated 5 days ago by 147k • written 6 days ago by • 0
1
vote
11
replies
2.8k
views
Microarray and RNA-seq different result
rna-seq microarray
updated 5 days ago by 36k • written 6.7 years ago by ▴ 550
2
votes
10
replies
2.9k
views
concatenate multiple GZip fastq files from multilane run and output combined gzip file
perl fastqc next-gen-sequencing
updated 5 days ago by 36k • written 6.7 years ago by ▴ 20
5
votes
10
replies
3.3k
views
Get multiple snps coverage (allelic depth) from bam files
bam sequencing genotype
updated 3 days ago by 36k • written 6.7 years ago by ★ 2.0k
10
votes
10
replies
11k
views
Download whole dataset from NCBI Taxonomy
NCBI Taxonomy
updated 5 days ago by 36k • written 6.7 years ago by ▴ 40
12
votes
10
replies
5.8k
views
CIBERSORT deconvolution advice
CIBERSORT CIBERSORTx deconvolution
updated 3 days ago by • 0 • written 2.4 years ago by ▴ 70
5
votes
10
replies
469
views
7 follow
Forum: Why isn't GWAS used in oncology?
gwas association oncology studies somatic cancer
updated 2 days ago by ▴ 600 • written 3 days ago by ▴ 70
6
votes
10
replies
5.1k
views
couting rpkm by edgr package
RNA-Seq rpkm R
updated 4 days ago by 36k • written 6.7 years ago by ★ 4.1k
11
votes
9
replies
7.7k
views
8 follow
Get number of variations in a huge VCF using Tabix?
vcf tabix big-data variation
updated 4 days ago by 36k • written 6.7 years ago by ▴ 520
5
votes
9
replies
3.2k
views
IGV view of bam file
igv
updated 5 days ago by 36k • written 6.7 years ago by ★ 1.4k
9
votes
9
replies
3.2k
views
variance stabilization and normalization
R
updated 3 days ago by 36k • written 6.7 years ago by ★ 4.1k
3
votes
9
replies
254
views
CellRanger runs into error when running fastq files from SRA
cellranger 10x single-cell sra
updated 3 days ago by 5.5k • written 3 days ago by ★ 1.4k
6
votes
9
replies
3.0k
views
Exon Center signal maps (metagene plots) using deepTools
ChIP-Seq metagene deepTools
updated 5 days ago by 36k • written 6.7 years ago by ▴ 60
7
votes
9
replies
8.5k
views
9 follow
How I do lift over a Plink bim file from Hg18 to Hg19.
plink SNP
updated 6 days ago by ▴ 10 • written 5.3 years ago by ▴ 680
0
votes
9
replies
3.0k
views
How to get sample names based on genotype from multi-sample vcf file
vcf
updated 5 days ago by 36k • written 6.7 years ago by ▴ 490
9
votes
9
replies
509
views
Which hg38 file?
reference hg38 NCBI
updated 2 days ago by ▴ 40 • written 14 days ago by ▴ 30
3
votes
9
replies
2.0k
views
Abyss-pe error at the final stage
abyss assembly
updated 3 days ago by 36k • written 6.7 years ago by ▴ 30
781 results • Page 1 of 16
Recent Votes
Why the result of GSEA and ssGSEA is different?
4-group RNAseq experiment- GSEA vs ssGSEA?
Are upset plots bad for differential expression analysis?
Answer: Are upset plots bad for differential expression analysis?
Answer: extracting sequences from a bam file
A: Best Genome Assembler and Genome Annotation tools and pipelines
Top/best RNAseq workflow including anlaysis results for function annotation
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Recent Replies
Comment: CWL and Arvados by dariober 13k
I've never used CWL and Arvados. However, snakemake, which I use quite extensively, has the option to export a workflow as [CWL](https://sn…
Comment: phylip format sequence name/header issue by Michael Dondrup 52k
MrBayes will complain if the first 15 characters of the sequences do not lead to unique taxa though.
Answer: phylip format sequence name/header issue by Mensur Dlakic ★ 20k
Phylip format can have an arbitrary number of characters in header, but not all the programs will tolerate it. MrBayes, for example, has no…
Answer: phylip format sequence name/header issue by Michael Dondrup 52k
I assume you have the sequences in a FASTA file. I recommend to shorten the sequences in FASTA format already, then convert to phylip forma…
Comment: Extract sequences from a list of ID by Neel ▴ 20
Thank you....It has been done.
Comment: SNV, CNA, SV by Vincent Laufer ★ 2.2k
what exactly do you want to show about them. do you want to show the order in which they arose? or epistasis between them> ? or any other p…
Comment: Why weblogo of biopython doesn't work? by Plus • 0
Yes. I can try the web version of WebLogo, but I just want to know what kind of problem can induce to make a corrupted file by using Motif.…
Comment: Difference between clusterProfiler and gProfileR by Arup Ghosh 3.0k
> The GO terms output by gprofileR are generally quite similar to those > output by clusterProfiler, but there are small differences due to…
Comment: hgmd variants from Ensembl by Sanjar ▴ 140
Did you figure out how to do this?
Comment: Why weblogo of biopython doesn't work? by Arup Ghosh 3.0k
The `weblogo` module uses the web version of weblogo service and it seems the module is not working as intended. Instead of returning an im…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ by appropiate ▴ 40
Thanks @cmdcolin! It looks great, but being relatively new on the field and having started with IGV, I think I will stick to the latter and…
Comment: Extract sequences from a list of ID by GenoMax 119k
You need to remove `>` from ID's as the warning tells you to do.
Comment: The best way to get gene lengths for 15K+ genes? by manaswwm ▴ 260
From my previous experiences in retrieving data in bulk from biomaRt/Ensembl - it is always better to partition your data into batches befo…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ by cmdcolin ★ 2.3k
disclaimer: I am a jbrowse 2 dev: you could consider jbrowse 2, which can load multiple genomes, visualize synteny, and look at the mapped …
Answer: download just a chromosome from SRA toolkit by ATpoint 64k
No, it is not possible since fastq are raw data without alignment information, hence without chromosomal information.
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