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1,000 results • Page 2 of 20
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121
votes
7
replies
119k
views
Bam And Indexed Bam Files
bam index
12.4 years ago by Sahel ▴ 260
120
votes
23
replies
31k
views
14 follow
Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
cram bam io hdf
updated 3.1 years ago by 44k • written 9.9 years ago by ▴ 320
120
votes
31
replies
200k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 6 months ago by 44k • written 14.1 years ago by 11k
120
votes
8
replies
80k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 2.4 years ago by 44k • written 9.7 years ago by ▴ 540
119
votes
25
replies
123k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 7.3 years ago by ▴ 160 • written 13.8 years ago by 5.0k
118
votes
26
replies
36k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 14 months ago by ▴ 210 • written 9.0 years ago by ▴ 610
118
votes
74
replies
46k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 18 months ago by 142k • written 13.5 years ago by ★ 3.3k
118
votes
15
replies
105k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 13.4 years ago by • 0 • written 13.5 years ago by ▴ 210
117
votes
18
replies
40k
views
14 follow
What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
education online
updated 7.1 years ago by ▴ 20 • written 12.8 years ago by ★ 1.3k
117
votes
59
replies
33k
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 15 months ago by 44k • written 9.0 years ago by ▴ 30
116
votes
25
replies
70k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 15 months ago by ▴ 20 • written 13.3 years ago by 162k
115
votes
21
replies
113k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 12.2 years ago by ▴ 30 • written 12.5 years ago by ★ 2.6k
114
votes
7
replies
28k
views
7 follow
What Makes One Probability Distribution Better For Rna-Seq Than Another?
rna
updated 13.2 years ago by ▴ 140 • written 13.2 years ago by 22k
112
votes
24
replies
47k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 21 months ago by 44k • written 13.0 years ago by ▴ 480
112
votes
56
replies
44k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 20 months ago by 44k • written 12.0 years ago by ▴ 380
110
votes
37
replies
8.6k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 15 months ago by 44k • written 12.7 years ago by 162k
108
votes
45
replies
87k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 20 months ago by ▴ 80 • written 11.8 years ago by ▴ 320
107
votes
27
replies
27k
views
12 follow
Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
python next-gen
updated 2.4 years ago by 44k • written 12.1 years ago by 11k
106
votes
27
replies
15k
views
14 follow
Is There Such A Thing As A Ucsc Api?
ucsc python comparative api
updated 3.0 years ago by ★ 1.6k • written 13.5 years ago by 2.3k
106
votes
12
replies
80k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 19 months ago by 44k • written 12.6 years ago by ★ 1.7k
105
votes
31
replies
95k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 5 months ago by ▴ 450 • written 12.9 years ago by ★ 5.1k
105
votes
21
replies
21k
views
19 follow
Why Should I Use Galaxy ?
galaxy workflow
7.1 years ago by Pierre Lindenbaum 162k
105
votes
81
replies
33k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 21 months ago by 142k • written 7.4 years ago by ★ 2.0k
105
votes
72
replies
18k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 5.6 years ago by 11k • written 13.8 years ago by 11k
105
votes
15
replies
113k
views
16 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 9 weeks ago by ▴ 140 • written 12.0 years ago by 12k
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 8 months ago by 11k • written 11.4 years ago by ▴ 810
103
votes
20
replies
30k
views
16 follow
What Wetlab Techniques Does A Bioinformatician Need To Be Able To Perform, If Any?
education meta
updated 13.2 years ago by ★ 1.6k • written 13.2 years ago by 3.2k
103
votes
27
replies
89k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 12 months ago by • 0 • written 12.0 years ago by ▴ 830
103
votes
34
replies
114k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 4 months ago by 44k • written 12.0 years ago by ▴ 390
102
votes
19
replies
18k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 15 months ago by 44k • written 12.0 years ago by ▴ 830
102
votes
44
replies
9.1k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 15 months ago by 44k • written 10.8 years ago by 24k
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 7 months ago by 44k • written 14.2 years ago by ★ 1.0k
102
votes
6
replies
63k
views
6 follow
Insert Size And Fragment Size ?
2.6 years ago by Nicolas Rosewick 11k
101
votes
9
replies
128k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 2.1 years ago by ▴ 40 • written 10.7 years ago by ▴ 760
100
votes
16
replies
78k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq coverage
9.5 years ago by Obi Griffith 20k
100
votes
12
replies
38k
views
14 follow
Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
somatic-mutation variant-calling SNV
updated 2.7 years ago by 44k • written 12.2 years ago by ★ 2.8k
99
votes
44
replies
24k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text r perl python
updated 6.7 years ago by ★ 2.6k • written 12.2 years ago by ★ 1.5k
99
votes
24
replies
17k
views
16 follow
Workflow management software for pipeline development in NGS
pipeline workflow
updated 2.3 years ago by 44k • written 9.6 years ago by ▴ 310
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
98
votes
12
replies
54k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 3.2 years ago by ▴ 10 • written 12.3 years ago by ▴ 420
97
votes
19
replies
94k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc fasta sequence
updated 7 months ago by 44k • written 14.3 years ago by 28k
97
votes
23
replies
33k
views
15 follow
Is Tophat The Only Mapper To Consider For Rna-Seq Data?
bwa tophat rna-seq
updated 2.0 years ago by 44k • written 11.4 years ago by ▴ 330
97
votes
35
replies
26k
views
16 follow
Disease Associated Snps
snp gwas database
updated 10.3 years ago by • 0 • written 14.0 years ago by ★ 1.5k
97
votes
26
replies
11k
views
15 follow
Do You Trust Bio-Xxx Projects ?
biopython bioperl biojava subjective
updated 13.3 years ago by 11k • written 13.3 years ago by ★ 2.2k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 6 months ago by 44k • written 14.1 years ago by 162k
95
votes
18
replies
71k
views
12 follow
Sequence length from Fasta
fasta
updated 17 months ago by 44k • written 9.5 years ago by ▴ 90
95
votes
21
replies
24k
views
13 follow
What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordinate Systems
coordinates genome
updated 9.5 years ago by 20 • written 13.2 years ago by 18k
95
votes
5
replies
55k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools clipped-reads soft-clip bam hard-clip
updated 2.4 years ago by 44k • written 9.8 years ago by ★ 2.5k
95
votes
6
replies
37k
views
In Sam Format, Clarify The Meaning Of The "0" Flag.
sam
updated 13.1 years ago by ★ 1.4k • written 13.1 years ago by ▴ 580
94
votes
50
replies
53k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 2.5 years ago by ▴ 20 • written 6.5 years ago by ▴ 220
1,000 results • Page 2 of 20
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Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Downloading NCBI Blast nt database
Comment: log2 fold change in RNA-seq analysis
Comment: log2 fold change in RNA-seq analysis
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
correct way of analyzing cell proportions in singlecell data
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Recent Replies
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…
Answer: 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.
Comment: minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of s by June • 0
Hello, I just started working on analyzing methylation EPIC array data using minfi. Data is generated on EPICv2 array and I'm using up…
Comment: Classic threshold for log2 fold change in RNA-seq experiment by Ram 44k
Please do not add answers unless you're actually answering the top level question. Open your own question if the forum has not addressed it…
Comment: log2 fold change in RNA-seq analysis by May Ling • 0
Thank you for your prompt reply Sir! I think I finally understand the concept. Please correct me if I'm wrong: Let's say we are comparing …
Comment: log2 fold change in RNA-seq analysis by Hatchet ▴ 10
He means that the result of DEA will contain DEGs of A vs B. He gets LFC numbers in one column and positive LFC numbers will mean positive …
Comment: Z score by Akash D ▴ 50
I made this. Z scored on log2FC? will anyone support me on this? 3 groups A,B,C
Comment: log2 fold change in RNA-seq analysis by i.sudbery 19k
There is no such thing as a fold change of -2. Fold change is expression_in_condition_A/expresssion_in_condition_B as expression is a…
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