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1,000 results • Page 2 of 20
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145
votes
56
replies
7.4k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 5 weeks ago by 38k • written 10.0 years ago by 97k
145
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 4 weeks ago by 38k • written 9.9 years ago by 5.9k
144
votes
62
replies
9.4k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 5 weeks ago by 38k • written 12.1 years ago by ★ 2.9k
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 13 days ago by 38k • written 5.3 years ago by 84k
143
votes
30
replies
126k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line command-line fasta list bash
updated 6 months ago by 38k • written 11.1 years ago by ★ 2.9k
143
votes
33
replies
27k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 4.0 years ago by ▴ 50 • written 12.8 years ago by 13k
143
votes
14
replies
20k
views
15 follow
What Are The Classic Papers In Bioinformatics?
literature papers history
updated 24 months ago by 21k • written 12.4 years ago by 18k
142
votes
14
replies
163k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 3.3 years ago by ★ 2.1k • written 13.0 years ago by 153k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 10 months ago by 38k • written 8.3 years ago by ★ 1.6k
138
votes
21
replies
67k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer gene database oncogene tumor
2.5 years ago by Malachi Griffith 19k
136
votes
25
replies
75k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 11 months ago by 38k • written 10.9 years ago by ★ 4.2k
136
votes
26
replies
23k
views
14 follow
Best Way For A Beginner To Get Up To Speed On Unix Quickly?
unix perl genomics
updated 5 weeks ago by 38k • written 11.2 years ago by ▴ 300
136
votes
41
replies
20k
views
20 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 4 weeks ago by 38k • written 9.8 years ago by ★ 1.6k
136
votes
29
replies
6.4k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 11 months ago by 38k • written 12.2 years ago by 21k
134
votes
65
replies
3.5k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate Forum
updated 13 months ago by 52k • written 3.3 years ago by ▴ 880
134
votes
13
replies
20k
views
Alignment and mapping
alignment next-gen mapping
updated 7.0 years ago by 8.3k • written 7.0 years ago by ▴ 700
133
votes
18
replies
154k
views
16 follow
Blast - Formatting Output
blast format output
updated 3 months ago by ▴ 20 • written 9.3 years ago by ▴ 310
131
votes
48
replies
14k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 11.6 years ago by ★ 2.6k • written 11.6 years ago by 11k
131
votes
27
replies
40k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 11 months ago by 38k • written 10.9 years ago by 33k
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 5 days ago by ★ 1.1k • written 4.4 years ago by 84k
130
votes
37
replies
12k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 11.6 years ago by ★ 1.3k • written 11.6 years ago by ▴ 820
129
votes
32
replies
122k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 11 months ago by 38k • written 12.1 years ago by ▴ 530
129
votes
38
replies
5.6k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics Forum
updated 4.0 years ago by 34k • written 4.0 years ago by 97k
128
votes
83
replies
9.9k
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
5.7 years ago by Petr Ponomarenko ★ 2.7k
127
votes
20
replies
49k
views
13 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 3.3 years ago by ▴ 220 • written 5.3 years ago by ★ 1.8k
127
votes
33
replies
53k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 5 months ago by 38k • written 8.9 years ago by ▴ 480
126
votes
44
replies
27k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 17 days ago by 38k • written 6.5 years ago by ▴ 970
126
votes
24
replies
74k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence length fastq
updated 3.9 years ago by • 0 • written 9.8 years ago by ▴ 360
124
votes
19
replies
171k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 23 months ago by • 0 • written 10.8 years ago by ▴ 350
124
votes
19
replies
23k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq alignment next-gen R assembly
updated 23 months ago by 38k • written 3.5 years ago by ▴ 720
124
votes
29
replies
6.2k
views
18 follow
What License Do You Use When You Release Code And Data?
general software subjective
updated 9.3 years ago by 20 • written 13.0 years ago by 7.4k
124
votes
46
replies
43k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq visualization deeptools ngsplot homer Forum
updated 20 months ago by ★ 2.3k • written 7.1 years ago by ★ 3.2k
122
votes
17
replies
70k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 12 months ago by 38k • written 11.9 years ago by ▴ 370
122
votes
11
replies
158k
views
11 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 19 months ago by • 0 • written 12.7 years ago by 4.8k
122
votes
42
replies
8.7k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 5 weeks ago by 38k • written 10.3 years ago by 97k
121
votes
44
replies
19k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 5 weeks ago by 38k • written 12.8 years ago by 5.3k
120
votes
8
replies
77k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 14 months ago by 38k • written 8.5 years ago by ▴ 520
119
votes
23
replies
28k
views
14 follow
Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
cram bam io hdf
updated 23 months ago by 38k • written 8.7 years ago by ▴ 320
118
votes
26
replies
32k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 16 days ago by ▴ 30 • written 7.9 years ago by ▴ 610
118
votes
31
replies
175k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 18 months ago by 127k • written 13.0 years ago by 11k
118
votes
7
replies
106k
views
Bam And Indexed Bam Files
bam index
11.2 years ago by Sahel ▴ 260
118
votes
15
replies
101k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 12.2 years ago by • 0 • written 12.4 years ago by ▴ 210
118
votes
53
replies
88k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 8 days ago by • 0 • written 8.8 years ago by ▴ 330
117
votes
25
replies
118k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 6.1 years ago by ▴ 160 • written 12.7 years ago by 4.8k
117
votes
59
replies
29k
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 6 weeks ago by 38k • written 7.9 years ago by ▴ 30
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 13 days ago by 38k • written 4.7 years ago by 70k
116
votes
31
replies
35k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 9 months ago by 38k • written 9.6 years ago by 11k
116
votes
35
replies
7.0k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 5 weeks ago by 38k • written 10.0 years ago by 21k
116
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 4 months ago by 127k • written 12.3 years ago by ★ 3.2k
115
votes
29
replies
28k
views
11 follow
PCA in a RNA seq analysis
RNA-Seq pca
updated 4.3 years ago by 27k • written 5.4 years ago by ▴ 330
1,000 results • Page 2 of 20
Recent Votes
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Popular Question to sharmatina189059 ▴ 110
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Recent Replies
Answer: Somatic truth set by samuel ▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold by ATpoint 70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat by Ming Tommy Tang ★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
Answer: how to know what adapter sequences to trim for RNA-seq? by Ming Tommy Tang ★ 2.9k
You may use fastp which detect adaptors by itself https://github.com/OpenGene/fastp#adapters
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