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867 results • Page 1 of 18
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118
votes
31
replies
190k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 15 days ago by 41k • written 13.6 years ago by 11k
142
votes
14
replies
167k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 18 days ago by 41k • written 13.6 years ago by 158k
76
votes
26
replies
112k
views
15 follow
How to count fastq reads
sequence next-gen fastq reads
updated 5 days ago by ★ 2.8k • written 8.6 years ago by ▴ 260
185
votes
43
replies
81k
views
29 follow
Drawing Chromosome Ideograms With Data
ideogram visualization chromosome
updated 21 days ago by 41k • written 13.7 years ago by ★ 1.6k
328
votes
54
replies
61k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 21 days ago by 41k • written 13.7 years ago by 24k
61
votes
23
replies
54k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 7 days ago by ★ 1.2k • written 10.8 years ago by ★ 1.3k
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 15 days ago by 158k • written 13.6 years ago by ▴ 660
74
votes
15
replies
35k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 15 days ago by 41k • written 13.6 years ago by 158k
78
votes
21
replies
34k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 12 days ago by • 0 • written 9.6 years ago by ▴ 650
23
votes
4
replies
34k
views
bcftools compressing and indexing vcf files
sequence bcftools vcf index
updated 23 days ago by 136k • written 5.2 years ago by ▴ 270
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 22 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 26 days ago by 41k • written 10.1 years ago by ★ 7.8k
48
votes
18
replies
31k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter sequence human genome
updated 15 days ago by 41k • written 13.6 years ago by ★ 1.6k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 18 days ago by 41k • written 13.6 years ago by 158k
100
votes
38
replies
29k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 6 days ago by 22k • written 10.0 years ago by ★ 3.6k
4
votes
9
replies
29k
views
8 follow
How To Get Chromosome Position Given Rs Number?
snp chromosome position
updated 15 days ago by 136k • written 10.0 years ago by • 0
172
votes
34
replies
25k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r books bioconductor
updated 21 days ago by 41k • written 13.7 years ago by 53k
22
votes
7
replies
24k
views
What Does The "N50" Mean?
assembly
updated 15 days ago by 41k • written 13.6 years ago by ★ 1.1k
39
votes
15
replies
22k
views
9 follow
How Do I Access And Query Entire Genome Sequences With R
gene r
updated 21 days ago by 41k • written 13.7 years ago by ▴ 790
89
votes
12
replies
20k
views
9 follow
What Do Different Bioinformatics Positions Mean?
career general
updated 21 days ago by 41k • written 13.7 years ago by ★ 1.6k
175
votes
46
replies
18k
views
26 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
9 days ago by Istvan Albert 99k
15
votes
9
replies
17k
views
8 follow
How to count fasta sequences efficiently using (or not ) biopython
biopython python fasta
updated 28 days ago by ★ 1.5k • written 5.8 years ago by ▴ 110
30
votes
18
replies
16k
views
8 follow
Is It Possible For Two Different Affymetrix Probe Set Id To Have Common Annotations To Same Gene ?
microarray annotation affymetrix probeset
updated 21 days ago by 41k • written 13.7 years ago by 18k
35
votes
10
replies
15k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq peak-calling
updated 15 days ago by 41k • written 13.6 years ago by ★ 1.4k
19
votes
16
replies
15k
views
6 follow
Conversion of Gene Name to Ensembl ID
gene RNA-Seq R genome
updated 27 days ago by ▴ 10 • written 3.7 years ago by ▴ 10
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software phylogenetics visualization
updated 21 days ago by 41k • written 13.7 years ago by ▴ 390
13
votes
11
replies
15k
views
10 follow
TCGA/Broad Institute CNV Files Segment Mean
tcga cnv
updated 4 days ago by ▴ 10 • written 9.2 years ago by ▴ 320
28
votes
13
replies
14k
views
7 follow
Create Consensus Sequences For Sequence Pairs Within A Multiple Alignment?
consensus phylogenetics fasta multiple-alignment
updated 18 days ago by 41k • written 13.6 years ago by ★ 2.0k
28
votes
27
replies
14k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython python fastq next-gen-sequencing
updated 18 days ago by 41k • written 13.6 years ago by 4.5k
20
votes
10
replies
14k
views
8 follow
Test Whether The Variance In A Group Is Lower Than In Another
statistics r
updated 21 days ago by 41k • written 13.7 years ago by 28k
2
votes
7
replies
13k
views
How too choose outgroup for rooting a phylogenetic tree?
phylogeny sequence alignment
updated 6 days ago by ▴ 30 • written 8.6 years ago by ★ 2.8k
25
votes
10
replies
13k
views
10 follow
Retrieve GFF3 file from ncbi
gff3 ncbi efetch
updated 26 days ago by ▴ 70 • written 5.8 years ago by ▴ 110
30
votes
6
replies
13k
views
What Are Some Good Free Bioinformatics And Computational Biology Books?
books online
updated 15 days ago by 41k • written 13.6 years ago by ★ 1.0k
17
votes
14
replies
13k
views
10 follow
Converting Ab1 Trace Files Into Scf Trace Files
sequence
updated 18 days ago by 41k • written 13.6 years ago by 4.5k
31
votes
8
replies
12k
views
Experiences With Clc Genomics Workbench (Or Other Commercial Tools) For Next-Gen Sequencing
next-gen-sequencing
updated 15 days ago by 41k • written 13.6 years ago by 99k
56
votes
12
replies
12k
views
9 follow
What Are The Public Sql Servers For Bioinformatics ?
online-server sql
updated 21 days ago by 41k • written 13.7 years ago by 158k
7
votes
8
replies
11k
views
7 follow
Makeblastdb Error In Blast+ 2.2.26
blast
updated 1 day ago by ▴ 50 • written 11.5 years ago by ▴ 40
25
votes
8
replies
11k
views
6 follow
Tools For Chipseq Scale Motif Finding?
motif motif chip-seq
updated 21 days ago by 41k • written 13.7 years ago by ★ 1.3k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 15 days ago by 41k • written 13.6 years ago by 18k
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 15 days ago by 41k • written 13.6 years ago by 28k
24
votes
9
replies
10k
views
6 follow
Exploring Snp Data
snp association
updated 15 days ago by 41k • written 13.6 years ago by ★ 1.1k
28
votes
14
replies
10k
views
7 follow
Compare Two Protein Sequences Using Local Blast
biopython blast
updated 21 days ago by 41k • written 13.7 years ago by ▴ 120
16
votes
4
replies
10k
views
Do P-Values From A Generalised Linear Model Need Correction For Multiple Testing?
statistics r multiple
updated 18 days ago by 41k • written 13.6 years ago by ★ 1.1k
24
votes
11
replies
10k
views
How To Download All Est Sequences For Organism Xx From Ncbi?
eutils genbank
updated 21 days ago by 41k • written 13.7 years ago by ★ 2.5k
14
votes
1
reply
10k
views
From A Geo Gsm Id, How To Obtain The Corresponding Raw File(S) Hosted On Sra?
fastq r bioconductor sra geo
updated 15 days ago by 41k • written 13.6 years ago by ▴ 190
27
votes
27
replies
10.0k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp allele biomart dbsnp
updated 21 days ago by 41k • written 13.7 years ago by 53k
21
votes
13
replies
9.9k
views
8 follow
Blast Motif With Regular Expression ?
blast motif
updated 15 days ago by 41k • written 13.6 years ago by ▴ 80
33
votes
9
replies
9.9k
views
10 follow
Which C++ Libraries Are Best For Dealing With Fastq Files?
next-gen-sequencing fastq c
updated 21 days ago by 41k • written 13.7 years ago by 22k
19
votes
15
replies
9.6k
views
12 follow
How To Split Reads For Different Flowcell Lanes In Fastq Files?
split reads
updated 28 days ago by ★ 3.4k • written 10.3 years ago by ▴ 750
46
votes
18
replies
9.5k
views
8 follow
Tips To Build A Data Storage For Bioinformatics
data
updated 21 days ago by 41k • written 13.7 years ago by 3.4k
867 results • Page 1 of 18
Recent Votes
Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
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Comment: unicycler error : [Errno 13] Permission denied:
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Recent Replies
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
> even if tpe and tbo are trailing after adapter and quality trimming Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads by cee28 • 0
Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by DINESHR • 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by dsull ★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM? by rpolicastro 12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks by Ankit ▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by cmdcolin ★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by rpolicastro 12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file by ATpoint 78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
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