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1,000 results • Page 2 of 20
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24
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44
replies
12k
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How to remove contamination from the transcriptome assembly
RNA-Seq contamination assembly blast Hiseq reads
updated 7 months ago by 38k • written 7.4 years ago by ★ 1.8k
152
votes
44
replies
28k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 8 months ago by 38k • written 9.2 years ago by ★ 2.0k
57
votes
43
replies
14k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
NGS alignment genome RNA-Seq sequence
updated 12 days ago by 38k • written 4.2 years ago by 9.9k
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 6 months ago by 38k • written 13.0 years ago by ★ 1.6k
59
votes
43
replies
18k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 7 days ago by 38k • written 5.5 years ago by ★ 1.4k
151
votes
42
replies
174k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 10 months ago by 38k • written 11.0 years ago by 20k
122
votes
42
replies
8.7k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 5 weeks ago by 38k • written 10.3 years ago by 97k
8
votes
42
replies
3.6k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 11 weeks ago by 38k • written 7.8 years ago by ▴ 290
78
votes
41
replies
28k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 3 months ago by • 0 • written 9.4 years ago by ★ 7.7k
136
votes
41
replies
20k
views
20 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 25 days ago by 38k • written 9.8 years ago by ★ 1.6k
16
votes
41
replies
7.7k
views
How to extract information from headers of fasta file
sequence
updated 9 months ago by 38k • written 8.0 years ago by ▴ 70
23
votes
41
replies
13k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 4 months ago by • 0 • written 5.2 years ago by ▴ 110
167
votes
41
replies
85k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence fasta
updated 7 weeks ago by • 0 • written 11.8 years ago by ▴ 240
18
votes
41
replies
10k
views
6 follow
paired end illumina reads
Assembly paired end
updated 8 months ago by 38k • written 7.4 years ago by ▴ 290
202
votes
41
replies
23k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 5 weeks ago by 38k • written 8.3 years ago by ★ 5.2k
17
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 7 days ago by 38k • written 6.7 years ago by ▴ 160
6
votes
40
replies
9.0k
views
Fastx_Collapser Has No Fastq Output
fastx RNA-seq
updated 21 days ago by 38k • written 9.5 years ago by ▴ 240
151
votes
39
replies
22k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 26 days ago by 38k • written 10.2 years ago by 3.0k
25
votes
39
replies
4.4k
views
8 follow
Forum: Bioinformatics Study Group
study-group
updated 22 days ago by 38k • written 9.7 years ago by ▴ 440
276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 10 months ago by 38k • written 8.6 years ago by 20k
81
votes
39
replies
6.0k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 5 weeks ago by 38k • written 10.2 years ago by 97k
226
votes
39
replies
281k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 7 months ago by 38k • written 13.4 years ago by ▴ 620
39
votes
38
replies
7.0k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 7 months ago by 38k • written 7.4 years ago by 13k
90
votes
38
replies
128k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 months ago by ▴ 10 • written 10.7 years ago by ▴ 370
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 11 months ago by 38k • written 8.1 years ago by ▴ 920
223
votes
38
replies
134k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 3 months ago by ▴ 90 • written 10.1 years ago by 19k
159
votes
38
replies
15k
views
22 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
updated 26 days ago by 38k • written 10.0 years ago by 97k
47
votes
37
replies
7.3k
views
12 follow
Forum: The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 22 days ago by 38k • written 9.6 years ago by 2.3k
110
votes
37
replies
6.9k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 5 weeks ago by 38k • written 11.5 years ago by 153k
49
votes
36
replies
7.2k
views
11 follow
Forum: New features and bug fixes for Biostar to work on during Google Summer of Code
meta biostars gsoc
updated 5 weeks ago by 38k • written 8.9 years ago by ▴ 110
59
votes
36
replies
34k
views
27 follow
Pca From Vcf Files
pca genome vcf
updated 7 months ago by ▴ 40 • written 10.9 years ago by ▴ 820
251
votes
36
replies
30k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
file
updated 6 months ago by 84k • written 12.9 years ago by 153k
8
votes
36
replies
9.9k
views
18 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 3 months ago by 38k • written 7.7 years ago by ▴ 160
9
votes
36
replies
2.6k
views
6 follow
GPL6883_HumanRef-8_V3_0_R0_11282963_A (illumina expression beadchip)
R
updated 4 months ago by ★ 1.8k • written 2.3 years ago by ▴ 30
99
votes
36
replies
27k
views
32 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 8 weeks ago by 21k • written 9.4 years ago by ★ 3.6k
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 26 days ago by 38k • written 10.3 years ago by ★ 1.6k
115
votes
35
replies
36k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow Forum
updated 11 days ago by ▴ 30 • written 5.8 years ago by ▴ 760
22
votes
35
replies
4.6k
views
Removing identifier with "unavailable sequence" from FASTA file
sequence genome blast RNA-Seq
updated 11 months ago by 38k • written 8.2 years ago by ★ 1.8k
45
votes
35
replies
4.6k
views
12 follow
Forum: looking for a bioinformatics project to do during military rotation
military
updated 8 months ago by 38k • written 5.6 years ago by ▴ 60
25
votes
35
replies
29k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 7 weeks ago by ▴ 10 • written 9.0 years ago by ★ 4.1k
4
votes
35
replies
7.8k
views
Is They Any Software Or Technique To Find The Number Of Reads Mapped To Each Contig After Aligment
mapping RNA-seq
updated 19 days ago by 38k • written 9.2 years ago by ▴ 50
65
votes
35
replies
18k
views
17 follow
Which Dna Compression Algorithms Are Actually Used?
dna
updated 6 months ago by 153k • written 11.8 years ago by ▴ 270
116
votes
35
replies
7.0k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 5 weeks ago by 38k • written 10.0 years ago by 21k
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 12 days ago by 38k • written 4.7 years ago by ★ 1.3k
54
votes
34
replies
3.6k
views
13 follow
Forum: Should We Release Database Dumps Of All Questions On Biostar?
meta biostars
updated 5 weeks ago by 38k • written 12.3 years ago by 97k
16
votes
34
replies
11k
views
6 follow
Why am I unable to load my data from a tab separated file into R?
microarray programming R
updated 11 months ago by 38k • written 8.1 years ago by ▴ 920
15
votes
34
replies
10k
views
Improving efficiency of awk for large files
awk
updated 4 months ago by 38k • written 7.7 years ago by ▴ 350
80
votes
34
replies
3.9k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 10 weeks ago by 38k • written 7.8 years ago by ▴ 520
145
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 25 days ago by 38k • written 9.9 years ago by 5.9k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
7 days ago by Ram 38k
1,000 results • Page 2 of 20
Recent Votes
Answer: trimmomatic on scRNA seq data
trimmomatic on scRNA seq data
10x 3' library creates R1 and R2 fastq files with the same read length
Answer: 10x 3' library creates R1 and R2 fastq files with the same read length
RNAseq: same reads + more complete scaffold = fewer DEGs?
Answer: GATK GenotypeGVCFs explain
A: Blast - Formatting Output
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Scholar to GenoMax 127k
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Recent Replies
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin? by GenoMax 127k
Based on the program name `run_pipeline.pl` this appears to be a perl script. Option you are referring to is for `Java`. Is that perl scrip…
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ? by GenoMax 127k
> So, I prefer to work assembled fastq files into one fastq rather than > two. What does this mean? Are you concatenating two sets of file…
Comment: What is exactly meant by "GENCODE TSS"? by ntsopoul ▴ 40
checkout: chipseeker package there is a function which gets you the tss getPromoters(TxDb=txdb, upstream=3000, downstream=3000) as you c…
Comment: SRA Taxonomy Analysis - difference between tables and web by GenoMax 127k
> Apparently it is ok for some accessions In that case, your best bet is to contact NCBI help desk with examples of what works and what do…
Comment: how to calcul risk score with a prognostic genes by Sarah ▴ 30
I did it manually. you multiply your gene expression by the coxPH coefficient.
Comment: Circos plot using vcf : Mutect2 MultiSample VCF out file by m. bioinfo • 0
thanks Pierre ! and I suspect this .bed output should be used as input for Circos. Do I need any corrections here ? 😊
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs? by Darked89 4.2k
Assuming that the genes are spliced and that new assembly => new annotation. One possibility is that previously counted as 2 or more gene f…
Comment: How to include spatial coordinate data into anndata within scanpy by Omics data mining ▴ 210
I am still struggling with this. I tried to add data manually, it gives me error. Would you please give me example to add spatial into h5a…
Comment: prefix extraction and preparation for mapping and variant calling by Joe 20k
You are explicitly specifying the suffixes in your commands, so it's entirely up to you if you stick to this, or you wish to define them ea…
Answer: GATK GenotypeGVCFs explain by Sarah ▴ 30
thank you all !
Comment: OrthoFinder problem by HERMAN ▴ 10
Hi Mike, It does not produce any error message, the software just freezes. I let it run for 1h without any improvement. I have come with…
Comment: What is exactly meant by "GENCODE TSS"? by Pierre Lindenbaum 153k
> How do you differentiate the case where for an alternate transcript of gene A, the first exon is NOT the first transcribed exon (due to s…
Comment: OrthoFinder problem by shelkmike ▴ 920
What error message does OrthoFinder produce?
Answer: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da by benformatics 3.5k
I would go with SUPPA2 or rMATS. You can see some benchmarking here: https://www.nature.com/articles/s41467-023-36585-y
Comment: CluserProfiler message "No gene can be mapped" by joe555 • 0
You were right. The author kindly replied and I also found this: https://github.com/YuLab-SMU/clusterProfiler/issues/561 The latest github…
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