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7,316 results • Page 2 of 147
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48
votes
20
replies
39k
views
16 follow
Generating consensus sequence from bam file
genome samtools bwa fasta
updated 11 weeks ago by ★ 1.3k • written 5.8 years ago by ▴ 70
48
votes
15
replies
18k
views
10 follow
DESeq2 compare all levels
differential-gene-expression RNA-Seq DESeq2
updated 8 months ago by • 0 • written 6.4 years ago by ★ 1.6k
47
votes
22
replies
36k
views
17 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 6 months ago by • 0 • written 11.2 years ago by ★ 5.3k
47
votes
13
replies
18k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 9 months ago by • 0 • written 4.2 years ago by 3.3k
47
votes
32
replies
20k
views
17 follow
Bwa Mem Have Different Alignment Result When Using Different Threads
updated 4 months ago by • 0 • written 10.9 years ago by ▴ 440
44
votes
12
replies
34k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 6 months ago by ▴ 170 • written 7.6 years ago by ▴ 240
43
votes
19
replies
74k
views
14 follow
Forum: Will A Masters In Bioinformatics Help Me In Getting A Job?
education career
updated 4 months ago by 44k • written 13.7 years ago by ▴ 50
42
votes
13
replies
29k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq DESeq2 geneontology GSEA
updated 9 months ago by ▴ 120 • written 7.1 years ago by ▴ 300
41
votes
16
replies
72k
views
16 follow
Converting Affymetrix Probes To Gene Ids
affymetrix conversion entrez
updated 5 months ago by • 0 • written 11.4 years ago by ▴ 140
41
votes
10
replies
48k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 7 months ago by ▴ 40 • written 7.3 years ago by ★ 1.4k
39
votes
24
replies
3.4k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 7 months ago by 20k • written 7 months ago by ▴ 590
39
votes
28
replies
11k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
10 months ago by Jeremy Leipzig 22k
39
votes
16
replies
41k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 11 months ago by 148k • written 4.3 years ago by ▴ 160
38
votes
26
replies
20k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq ChIP-Seq GO gene ontology
written 8.8 years ago by ▴ 370
38
votes
12
replies
19k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed ensembl bedops gtf
updated 9 months ago by 36k • written 8.3 years ago by ▴ 260
36
votes
13
replies
7.6k
views
8 follow
How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Performed
data galaxy
written 13.6 years ago by ▴ 520
36
votes
11
replies
48k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 11 months ago by 44k • written 12.6 years ago by ▴ 160
36
votes
25
replies
36k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen RNA-Seq
updated 11 months ago by ▴ 60 • written 10.3 years ago by ▴ 90
36
votes
12
replies
1.2k
views
11 follow
Forum: How to improve a bioinformatics study and paper so that it is not considered "too preliminary" by publishers and journals?
DEG journal
updated 4 months ago by 5.0k • written 4 months ago by ▴ 60
36
votes
14
replies
2.0k
views
9 follow
Forum: Good Bioinformatics Jokes/Puns?
bioinformatics
updated 5 months ago by 12k • written 5 months ago by ▴ 20
35
votes
17
replies
17k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
R classification cancer randomForest machine-learning
4 months ago by Obi Griffith 20k
35
votes
16
replies
22k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 7 months ago by ▴ 10 • written 10.8 years ago by ▴ 180
35
votes
15
replies
14k
views
10 follow
How to select an aligner?
RNA-Seq next-gen alignment
updated 11 months ago by • 0 • written 6.5 years ago by ▴ 730
35
votes
6
replies
32k
views
How bcftools isec works ?
vcf variant intersection bcftools
updated 5 months ago by 44k • written 9.7 years ago by ★ 2.4k
34
votes
24
replies
5.8k
views
8 follow
Forum: Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF file-format genomics
5 months ago by LauferVA 4.5k
34
votes
16
replies
21k
views
14 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 months ago by ▴ 70 • written 8.2 years ago by ▴ 310
34
votes
6
replies
42k
views
Blast Settings For Short Sequences
blast
updated 7 weeks ago by ▴ 140 • written 12.5 years ago by ▴ 360
33
votes
4
replies
43k
views
Raw counts to TPM in R
RNA-Seq R
updated 5 months ago by 85k • written 6.3 years ago by ★ 1.6k
33
votes
12
replies
2.3k
views
7 follow
Forum: Nextflow and self-made pipelines opinion
nextflow pipeline data-analysis
9 months ago by karlaarz ▴ 110
32
votes
13
replies
10k
views
11 follow
Any Recommendations For Statistical Genetics Texts?
genetics statistics gwas
updated 11 months ago by • 0 • written 14.3 years ago by ▴ 180
31
votes
14
replies
25k
views
7 follow
Difference between tSNE and PCA analysis
next-gen rna-seq
updated 9 months ago by 22k • written 6.9 years ago by ▴ 160
31
votes
13
replies
12k
views
9 follow
Variant Function Prediction
variant-effect SNP
updated 3 months ago by 44k • written 10.7 years ago by ▴ 360
31
votes
23
replies
31k
views
15 follow
Amino Acid Change To Genomic Location
snp amino-acids
updated 11 months ago by ▴ 120 • written 12.9 years ago by ▴ 110
31
votes
8
replies
9.0k
views
9 follow
Notepad and word will not read Fastq or FASTA files
software-error fastq
written 9.7 years ago by • 0
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna rRNA metagenomics
updated 8 months ago by 44k • written 14.1 years ago by ▴ 650
30
votes
12
replies
4.4k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 7 months ago by 44k • written 4.6 years ago by ▴ 330
29
votes
10
replies
7.1k
views
10 follow
Forum: Interesting/useful/beautiful bio sequence viz tools
viz python visualisation
updated 5 months ago by ★ 2.5k • written 6.7 years ago by 21k
29
votes
28
replies
37k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 7 months ago by • 0 • written 13.4 years ago by ★ 1.7k
28
votes
20
replies
23k
views
7 follow
how do I run repeat masker
repeatmasker
updated 10 months ago by 11k • written 9.0 years ago by ▴ 80
28
votes
11
replies
35k
views
10 follow
Samtools View: Only Forward Or Reverse Strand
samtools strand
updated 10 months ago by • 0 • written 13.1 years ago by ▴ 540
28
votes
9
replies
47k
views
Converting Gff To Bed With Bedtools?
gff bed bedtools
updated 10 months ago by 44k • written 11.9 years ago by ▴ 950
28
votes
7
replies
11k
views
9 follow
Add contig lenght to VCF header in a robust way
vcf
updated 10 days ago by ▴ 760 • written 8.5 years ago by ★ 5.3k
28
votes
8
replies
16k
views
Use samtools index on multiple bam files at the same time from the command line?
RNA-Seq next-gen sequence
updated 3 months ago by 164k • written 9.0 years ago by ▴ 510
27
votes
8
replies
11k
views
7 follow
Any Quick Sort Method For Large Bed File As 20G In Size?
sort bed
updated 10 months ago by ▴ 540 • written 11.7 years ago by ▴ 310
27
votes
9
replies
39k
views
7 follow
How To Extract Set Of Reads From Fastq (Or Eventually Fasta And Qual) Based On List Of Ids?
extraction read 454 fastq fasta
updated 3 months ago by 148k • written 12.6 years ago by 3.2k
27
votes
35
replies
3.2k
views
Indexing a 2.6GB Plant Genome Using STAR (genomeGenerate Mode) Terminated Due to RAM Limit — Can the Genome Be Split for Indexing, or Are There Other…
star RAN-seq bam genome indexing
updated 11 days ago by ★ 2.8k • written 4 weeks ago by ▴ 90
27
votes
8
replies
1.8k
views
6 follow
Forum: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
genomics snps survey papers
updated 5 months ago by 6.9k • written 12 months ago by ★ 1.4k
26
votes
5
replies
25k
views
BLAST options: max_target_seqs and num_alignments
blast
updated 8 months ago by ▴ 30 • written 10.1 years ago by ★ 1.4k
26
votes
10
replies
23k
views
6 follow
What is the best way to rank genes for GSEA?
GSEA GO Gene ranking RNA-Seq
updated 8 weeks ago by ▴ 60 • written 5.6 years ago by ▴ 170
26
votes
27
replies
3.2k
views
10 follow
Forum: Determining computer time required
computer hpc time
updated 10 months ago by ★ 6.9k • written 11 months ago by ▴ 40
7,316 results • Page 2 of 147
Recent Votes
Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
Comment: HLA alignment, approximation and frequencies
Comment: SnpEff Query
Comment: SnpEff Query
Merging CRAM files
Answer: Merging CRAM files
Answer: Merging CRAM files
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Recent Replies
Answer: model interaction in DeSeq2 with >1K samples by i.sudbery 20k
In their discussion of doing single cell RNAseq, which also often has a large number of samples, the DESeq2 authors recommend using glmGamP…
Answer: Concatenating all unmapped or alternative contigs in a reference genome by Semir ▴ 20
I'd also like to share an alternative answer that might be less cryptic than the sed command: # First concatenate all fa files in th…
Comment: Feature Counts - potential bug with outfile.jcounts by GenoMax 148k
Tagging https://www.biostars.org/u/13578/ <!-- this is nothing -->
Comment: HLA alignment, approximation and frequencies by oumo • 0
Thank you Let me check out these specialized tools
Comment: Feature Counts - potential bug with outfile.jcounts by chrisk • 0
Thanks for the comment @GenoMax. We too note, those genes are on opposite strands. For context, we have an unstranded library. Cheers, C…
Comment: Feature Counts - potential bug with outfile.jcounts by GenoMax 148k
These two genes are on opposite strands. Based on your command you appear to have unstranded data or are doing the counting with that setti…
Comment: Refseq1405.40 and hisat2-build (-ss and --exon) by chrisk • 0
Hello Biostars community, For anyone else whom this issue may concern, It was obviated with a bare metal install of Linux. We did not hea…
Answer: log transformation before imputation (impute.knn) in proteomic data? by KABILAN ▴ 130
By which normalization method you have applied to the dataset? Since normalization and imputation methods are data-specific in nature, yo…
Answer: Spatial correlation between two continuous variables by dsull ★ 6.9k
Looks at bivariate metrics like Lee’s L https://link.springer.com/article/10.1007/s101090100064
Comment: Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure by dsull ★ 6.9k
I just edited my post above to make it more intuitive+coherent (it was 3AM in Los Angeles last night when I wrote my initial post).
Comment: Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM value by dsull ★ 6.9k
The URL you linked to only has "batch normalized" expression. Unfortunately, there is no way to undo batch normalization to recover TPM val…
Comment: vg mod changes a graph, but what about a gam or gamp to the original graph? by joseph.fass ▴ 10
I thought I could just select alignments from the GAMP in a filter command, outputting a single-path (mostly) GAMP, then convert to GAM. Th…
Comment: IGV is not showing all alignments of SAM file by gernophil ▴ 120
Thanks for all your efforts. I will report this tomorrow and use BAM files for now :).
Comment: vg mod changes a graph, but what about a gam or gamp to the original graph? by Jordan M Eizenga ▴ 650
You are correct that this would invalidate the GAM. It's a tricky problem, and I actually don't think that compacting the nodes would help …
Comment: IGV is not showing all alignments of SAM file by GenoMax 148k
So it would be best for OP to report it via IGV help channel: https://groups.google.com/g/igv-help
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