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Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen sequencing parsing fastq programming
updated 2.3 years ago by 44k • written 13.3 years ago by ★ 2.2k
57
votes
43
replies
16k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
NGS alignment genome RNA-Seq sequence
updated 14 months ago by 44k • written 5.3 years ago by 11k
138
votes
42
replies
22k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 14 months ago by 4.2k • written 11.0 years ago by ★ 1.6k
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 6 weeks ago by 22k • written 10.5 years ago by ★ 3.6k
11
votes
42
replies
4.2k
views
over presented kmer in fastq
fastqc RNA-Seq
6.6 years ago by Sam ▴ 150
57
votes
42
replies
6.7k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 2.3 years ago by 44k • written 9.6 years ago by 33k
152
votes
42
replies
181k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 2.0 years ago by 44k • written 12.2 years ago by 20k
28
votes
42
replies
7.2k
views
7 follow
How to add tophat and bowtie to the path?
export PATH bowtie2.2.9 tophat2
7.5 years ago by mirza ▴ 180
8
votes
42
replies
4.8k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 16 months ago by 44k • written 9.0 years ago by ▴ 290
23
votes
41
replies
4.5k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS biopython illumina WGS
updated 12 months ago by 44k • written 13 months ago by ▴ 30
31
votes
41
replies
2.8k
views
12 follow
Forum: Question regarding journal publications
publications journals
updated 11 months ago by 44k • written 4.2 years ago by ▴ 40
19
votes
41
replies
9.3k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 6.8 years ago by ★ 5.2k • written 6.8 years ago by ▴ 80
26
votes
41
replies
17k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 18 months ago by • 0 • written 6.4 years ago by ▴ 120
98
votes
41
replies
6.3k
views
17 follow
Forum: I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error next-gen-sequencing
updated 13 months ago by 44k • written 7.7 years ago by ▴ 510
18
votes
41
replies
14k
views
6 follow
paired end illumina reads
Assembly paired end
updated 22 months ago by 44k • written 8.6 years ago by ▴ 290
18
votes
41
replies
3.7k
views
6 follow
Convert amino acid sequences into nucleotide sequences
nucleotide protein
updated 5 months ago by 21k • written 7 months ago by ▴ 40
5
votes
41
replies
3.0k
views
Insert sequence in nt database
nt
4.0 years ago by anasofiamoreira94 ▴ 80
38
votes
41
replies
60k
views
9 follow
Volcano Plot from DEseq2
R
written 6.5 years ago by ★ 1.2k
16
votes
41
replies
9.7k
views
How to extract information from headers of fasta file
sequence
updated 23 months ago by 44k • written 9.2 years ago by ▴ 70
171
votes
41
replies
98k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 8 months ago by 44k • written 12.9 years ago by ▴ 250
13
votes
41
replies
2.4k
views
Is my file created completely
sam BWA-MEM BWA
updated 14 months ago by 44k • written 7.0 years ago by ▴ 10
203
votes
41
replies
25k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 15 months ago by 44k • written 9.5 years ago by ★ 5.3k
18
votes
40
replies
19k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.9 years ago by • 0 • written 7.9 years ago by ▴ 170
40
votes
40
replies
11k
views
9 follow
What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
ATAC-seq alignment
updated 6.2 years ago by 88k • written 7.6 years ago by ▴ 560
16
votes
40
replies
6.4k
views
About TCGA CNV data preprocessing
SNP CNV
updated 5.6 years ago by 88k • written 5.6 years ago by ▴ 50
6
votes
40
replies
11k
views
Fastx_Collapser Has No Fastq Output
fastx RNA-seq
updated 15 months ago by 44k • written 10.7 years ago by ▴ 240
68
votes
40
replies
6.5k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen sequencing sequencing
updated 12.6 years ago by ▴ 310 • written 12.6 years ago by ★ 1.3k
10
votes
40
replies
6.6k
views
weird insert size post trimming
RNA-Seq
updated 6.8 years ago by ★ 2.9k • written 6.8 years ago by ▴ 290
67
votes
40
replies
9.8k
views
12 follow
Forum: I want to re-open the old debate: python or perl ?
perl python
updated 2.3 years ago by 44k • written 9.5 years ago by ★ 2.9k
151
votes
39
replies
25k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 15 months ago by 44k • written 11.3 years ago by 3.0k
20
votes
39
replies
10.0k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast blast memory
updated 8.7 years ago by ▴ 170 • written 12.4 years ago by ▴ 160
25
votes
39
replies
5.9k
views
8 follow
Forum: Bioinformatics Study Group
study-group
updated 15 months ago by 44k • written 10.9 years ago by ▴ 440
69
votes
39
replies
4.8k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 12 months ago by 44k • written 7.0 years ago by 13k
98
votes
39
replies
159k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 13 months ago by ▴ 180 • written 11.9 years ago by ▴ 390
288
votes
39
replies
184k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 14 months ago by 44k • written 9.7 years ago by 20k
66
votes
39
replies
7.6k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career subjective
updated 3.2 years ago by 44k • written 14.2 years ago by ▴ 310
18
votes
39
replies
4.4k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 12 months ago by 44k • written 5.1 years ago by ▴ 50
55
votes
39
replies
5.8k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf python perl awk
updated 11.7 years ago by 8.3k • written 11.7 years ago by ▴ 310
81
votes
39
replies
7.7k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 15 months ago by 44k • written 11.4 years ago by 100k
226
votes
39
replies
289k
views
33 follow
Gene Id Conversion Tool
david
updated 7 months ago by 44k • written 14.6 years ago by ▴ 620
36
votes
39
replies
4.2k
views
11 follow
Forum: Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast RNA-Seq alignment next-gen-sequencing
updated 12 months ago by 44k • written 6.5 years ago by ▴ 130
11
votes
39
replies
4.2k
views
Any advice for a de novo genome assembly
k-mer de novo genome assembly
updated 7.5 years ago by ▴ 60 • written 7.5 years ago by ▴ 640
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 2.1 years ago by 44k • written 9.3 years ago by ▴ 920
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 11 weeks ago by ▴ 60 • written 7.9 years ago by 6.6k
53
votes
38
replies
4.6k
views
10 follow
Multiple alignment software
alignment clustal omega tcoffee
updated 4.7 years ago by 100k • written 4.7 years ago by ▴ 130
27
votes
38
replies
20k
views
Heatmap based with FPKM values
RNA-Seq next-gen R
updated 5.0 years ago by 20 • written 6.5 years ago by ▴ 820
48
votes
38
replies
17k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 13 months ago by 44k • written 8.2 years ago by 11k
231
votes
38
replies
147k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 11 months ago by 44k • written 11.2 years ago by 20k
39
votes
38
replies
9.1k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 21 months ago by 44k • written 8.5 years ago by 13k
129
votes
38
replies
8.4k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 11 months ago by 44k • written 5.1 years ago by 100k
117,108 results • Page 3 of 2343
Recent Votes
A: VCF files: Change Chromosome Notation
Comment: Z score
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
A: VCF files: Change Chromosome Notation
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Popular Question to Erika • 0
Teacher to GenoMax 142k
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Recent Replies
Comment: What is a good way to do gene differentials in single cell data where one group by ATpoint 82k
I would keep it transparent. Do DE by subsetting large to small group. Do that randomly many times, then either average stats or use some s…
Answer: Trying to understand warning from MACS2 about too few paired peaks and differing by jared.andrews07 ★ 17k
Without looking at the actual sequence for each genome, my guess is that the Echinobase reference just matches much more closely to the org…
Comment: What do the transcript variant # mean in RefSeq? by Ram 44k
> It does not seem to be the longest transcript. Is it the canonical transcript? Longest == canonical. If you're looking for the transcrip…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx by Shicheng Guo ★ 9.4k
Hi ATpoint, Thank you for your responses. My apologies if my inquiries have seemed one-sided. I greatly value the collaborative spirit of t…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx by ATpoint 82k
Team? A team helps each other out. You only take help by posting your regular lazy do-my-work questions and never give anything back. Save …
Comment: What do the transcript variant # mean in RefSeq? by GenoMax 142k
> What do these correspond to? It does not seem to be the longest transcript. Is it the canonical transcript? Those are just different tra…
Answer: Mouse or Rat Gene Expression Data Similar to GTEx by jared.andrews07 ★ 17k
MGI has a [Gene Expression Database](https://www.informatics.jax.org/expression.shtml) that'll largely get you what you want.
Comment: Difference in Bismark output methylation call files and coverage files by Papyrus ★ 2.9k
Your files end in `CpG_report` so they are the "genome-wide cytosine report output". If you look at the [Bismark documentation][1] you will…
Comment: Error when looping over multiple columns in a data frame in R by Mohamed Samir ▴ 30
Dear Jeremy, Thanks. What I could not understand why you wrote it like : cutpoint_results[[col_name]] ? Is it because it is a list result…
Comment: BEAST2.5 Chloroplast Divergence Time using Fossil Records by Ram 44k
Do not use all caps - it's bad etiquette. I've fixed things for you this time.
Comment: minfi::getQC - badsamplecutoff 10.5 by Papyrus ★ 2.9k
I've recently also analyzed EPICv2 and have noticed that the log2 median intensities (and particularly the "uMed" channel), for an otherwis…
Comment: log2 fold change in RNA-seq analysis by May Ling • 0
Thank you so much for the confirmation Sir! Appreciate that. I think the paragraph was trying to say that: a fold change greater than **…
Comment: Difference in Bismark output methylation call files and coverage files by skdv2522 • 0
Chr1 192 + 0 0 CG CGA Chr1 193 - 0 0 CG CGA Chr1 197 + 0 0 CG CGT Chr1 198 - 0 0 CG CGG Chr1 218 + 0 0 CG CGA Chr1 …
Comment: Error with BiocParallel. No barcodes files found by Pierre Lindenbaum 162k
cross-posted: https://stackoverflow.com/questions/78522566/ > Do not post on multiple forums - that is just bad etiquette. What's worse, y…
Comment: log2 fold change in RNA-seq analysis by dsull ★ 6.1k
Your understanding is correct. That attached highlighted sentence is wrong.
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