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1,000 results • Page 2 of 20
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145
votes
56
replies
7.1k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostar Forum
updated 9.3 years ago by 49k • written 9.5 years ago by 94k
144
votes
62
replies
8.9k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
biostar meta statistics Forum
updated 5.3 years ago by 52k • written 11.6 years ago by ★ 2.9k
143
votes
34
replies
50k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation maf tcga cancer music Tutorial
updated 4 months ago by 37k • written 9.5 years ago by 5.8k
143
votes
33
replies
26k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 3.5 years ago by ▴ 50 • written 12.3 years ago by 13k
143
votes
14
replies
19k
views
15 follow
What Are The Classic Papers In Bioinformatics?
literature papers history
updated 18 months ago by 21k • written 11.9 years ago by 18k
142
votes
21
replies
28k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 5 months ago by 37k • written 7.8 years ago by ★ 1.6k
141
votes
68
replies
40k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 3 months ago by • 0 • written 4.9 years ago by 83k
139
votes
30
replies
119k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line command-line fasta list bash
updated 21 days ago by 37k • written 10.6 years ago by ★ 2.9k
138
votes
14
replies
160k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 2.9 years ago by ★ 2.1k • written 12.5 years ago by 149k
136
votes
26
replies
23k
views
14 follow
Best Way For A Beginner To Get Up To Speed On Unix Quickly?
unix genomics perl tutorial
updated 9.4 years ago by 5.7k • written 10.7 years ago by ▴ 300
136
votes
21
replies
66k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer gene database oncogene tumor
24 months ago by Malachi Griffith 19k
136
votes
29
replies
6.2k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 5 months ago by 37k • written 11.8 years ago by 21k
135
votes
41
replies
20k
views
20 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Forum
updated 9.0 years ago by ★ 1.1k • written 9.3 years ago by ★ 1.6k
134
votes
65
replies
3.0k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate Forum
updated 8 months ago by 52k • written 2.8 years ago by ▴ 830
132
votes
25
replies
71k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 6 months ago by 37k • written 10.4 years ago by ★ 4.2k
131
votes
48
replies
13k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 11.2 years ago by ★ 2.5k • written 11.2 years ago by 11k
131
votes
27
replies
39k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 5 months ago by 37k • written 10.5 years ago by 33k
130
votes
37
replies
11k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 11.1 years ago by ★ 1.3k • written 11.1 years ago by ▴ 820
129
votes
32
replies
119k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 6 months ago by 37k • written 11.6 years ago by ▴ 530
129
votes
38
replies
5.1k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics Forum
updated 3.5 years ago by 34k • written 3.5 years ago by 94k
128
votes
83
replies
9.3k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
fastq compressor lossless fastq compression Tool
5.2 years ago by Petr Ponomarenko ★ 2.7k
126
votes
122
replies
25k
views
23 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 29 days ago by • 0 • written 4.0 years ago by 83k
126
votes
19
replies
147k
views
14 follow
Blast - Formatting Output
blast format output
updated 2.0 years ago by • 0 • written 8.8 years ago by ▴ 300
126
votes
44
replies
26k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
RNA-Seq NGS adapter Forum
written 6.1 years ago by ▴ 910
124
votes
24
replies
69k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence length fastq
updated 3.4 years ago by • 0 • written 9.4 years ago by ▴ 360
124
votes
29
replies
5.9k
views
18 follow
What License Do You Use When You Release Code And Data?
general software subjective
updated 8.8 years ago by 20 • written 12.6 years ago by 7.4k
124
votes
46
replies
40k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq visualization deeptools ngsplot homer Forum
updated 14 months ago by ★ 2.3k • written 6.6 years ago by ★ 3.2k
123
votes
33
replies
47k
views
18 follow
VCF files: Change Chromosome Notation
next-gen sequence
updated 3 months ago by ▴ 30 • written 8.5 years ago by ▴ 480
123
votes
13
replies
18k
views
Alignment and mapping
alignment next-gen mapping
updated 6.6 years ago by 8.3k • written 6.6 years ago by ▴ 670
122
votes
17
replies
67k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 6 months ago by 37k • written 11.4 years ago by ▴ 370
122
votes
42
replies
8.4k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
biostar meta News
updated 5.8 years ago by ▴ 380 • written 9.9 years ago by 94k
121
votes
44
replies
18k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
job subjective
updated 6.3 years ago by 10k • written 12.3 years ago by 5.3k
121
votes
20
replies
43k
views
13 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 2.8 years ago by ▴ 210 • written 4.9 years ago by ★ 1.8k
121
votes
11
replies
150k
views
11 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 13 months ago by • 0 • written 12.2 years ago by 4.8k
120
votes
8
replies
76k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 9 months ago by 37k • written 8.0 years ago by ▴ 520
120
votes
19
replies
166k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 17 months ago by • 0 • written 10.3 years ago by ▴ 340
119
votes
23
replies
27k
views
14 follow
Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
cram bam io hdf
updated 18 months ago by 37k • written 8.2 years ago by ▴ 320
118
votes
31
replies
159k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 12 months ago by 121k • written 12.5 years ago by 11k
118
votes
15
replies
100k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 11.7 years ago by • 0 • written 11.9 years ago by ▴ 210
117
votes
59
replies
28k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware next-gen
updated 1 day ago by 37k • written 7.4 years ago by ▴ 30
116
votes
31
replies
34k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 3 months ago by 37k • written 9.1 years ago by 11k
116
votes
35
replies
6.5k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
biostar Forum core
updated 3.5 years ago by 13k • written 9.5 years ago by 21k
116
votes
68
replies
40k
views
37 follow
Is there a Lims that doesn't suck?
LIMS
updated 18 months ago by 94k • written 11.8 years ago by ★ 3.2k
115
votes
7
replies
100k
views
Bam And Indexed Bam Files
bam index
10.8 years ago by Sahel ▴ 240
115
votes
21
replies
110k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 10.5 years ago by ▴ 30 • written 10.9 years ago by ★ 2.6k
115
votes
18
replies
37k
views
14 follow
What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
education online
updated 5.4 years ago by ▴ 20 • written 11.2 years ago by ★ 1.3k
114
votes
29
replies
25k
views
11 follow
PCA in a RNA seq analysis
RNA-Seq pca
updated 3.9 years ago by 27k • written 4.9 years ago by ▴ 320
114
votes
25
replies
31k
views
20 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
Salmon DESeq DESeq2 RNASeq Kallisto
updated 7.4 years ago by ★ 2.5k • written 7.4 years ago by ▴ 590
114
votes
66
replies
37k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera ENA fastq-dump Tutorial Fastq
3 months ago by ATpoint 65k
114
votes
52
replies
81k
views
21 follow
How to plot coverage and depth statistics of a bam file
sequencing coverage bam depth next-gen
updated 9 weeks ago by • 0 • written 8.3 years ago by ▴ 320
1,000 results • Page 2 of 20
Recent Votes
Answer: Unaligned Reads From Bowtie2
Four NCBI workshops in October (BLAST, Primer-BLAST, Metagenome analysis, Structures in iCn3D)
A: PLINK vcf to binary files error: Unused command line option: --vcf
PLINK vcf to binary files error: Unused command line option: --vcf
Answer: Parsing a genebank file and tsv file - extracting and outputting specific data t
Four NCBI workshops in October (BLAST, Primer-BLAST, Metagenome analysis, Structures in iCn3D)
haplotype phasing in duos
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Recent Replies
Answer: empty peaks count, ChIP-seq, filter Bam, bed, bigwig, threshold, false peaks by maverenia • 0
I quess the problem is that I don't see the weak peaks in bigwigs, but they are counted in bed files. I there some approach to get bigwigs …
Comment: High number of unmapped reads in STAR by Negara • 0
yes in both the chromosome names are in the same format as chr1, chr2, etc.
Comment: Unaligned Reads From Bowtie2 by tiziana • 0
thank you for your answer. sorry if mine is a stupid question, as i am quite new to this, what does it mean "what is expected based on libr…
Answer: empty peaks count, ChIP-seq, filter Bam, bed, bigwig, threshold, false peaks by maverenia • 0
For the MACS2 callpeak I use the following conditions: Set lower mfold bound - 5 Set upper mfold bound - 50 Band width for picking regio…
Answer: How to convert Ensemble Gene IDs to gene symbols or Entrez Gene IDs? by Laura Luebbert ▴ 240
gget info https://github.com/pachterlab/gget
Comment: Parsing a genebank file and tsv file - extracting and outputting specific data t by Zach G • 0
Thank you very much. This is helpful. Now I tried implementing the code and it did give me a NameError: name 'category' not defined referri…
Comment: For loop rna sequencing alignment by iraun 4.7k
`404: Error Not Found` (Now seriously, you forgot to copy the error ;) ) So far the only thing that I can see is that the `done` in the e…
Answer: Why 6mA data are always 41 bps long? by acvill ▴ 160
The paper you reference ([Chen *et al*. 2019](https://doi.org/10.1093/bioinformatics/btz015)) includes the following excerpt, emphasis mine…
Answer: DEXseq estimateDispersions() returns error `replacement has 1 row, data has 0` by tien ▴ 10
I know the reason now. DESeqDataSet will automatically calculate count of other bins and generat column sample in colData. Previously, I ma…
Comment: For loop rna sequencing alignment by Pierre Lindenbaum 149k
not an answer but : you'd better use a workflow manager like snakemake or nextflow. > ..I am getting this error what is "this error" ?
Answer: Mapping PDB ID + chain ID to UniProt ID by Wayne ★ 1.4k
### Issue with pypdb route The pypdb route fails because the API pypdb access changed that it uses so that [the information no longer incl…
Comment: Parsing a genebank file and tsv file - extracting and outputting specific data t by Andrzej Zielezinski 11k
Thanks - now I understood. Please see my answer.
Answer: Parsing a genebank file and tsv file - extracting and outputting specific data t by Andrzej Zielezinski 11k
The following code produces the output you provided. Hope you find this code helpful. from Bio import SeqIO GBK_FILE = 'input…
Answer: Mapping PDB ID + chain ID to UniProt ID by Jiyao Wang ▴ 220
You can use an API from SIFT and parse the JSON output, e.g., https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/1kq2
Comment: Parsing a genebank file and tsv file - extracting and outputting specific data t by Zach G • 0
Great. So that is actually purposeful that there are no sequence ids common between the files. The idea is to add the sequence id's from bo…
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