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1,000 results • Page 2 of 20
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84
votes
16
replies
86k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 6 months ago by ▴ 50 • written 8.1 years ago by ★ 2.6k
238
votes
176
replies
85k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 3 days ago by 39k • written 7.8 years ago by ★ 4.6k
101
votes
31
replies
83k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 10 months ago by 39k • written 11.9 years ago by ★ 5.0k
79
votes
22
replies
83k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen sequencing fasta rna r perl
updated 6 months ago by 39k • written 11.6 years ago by ▴ 290
55
votes
11
replies
81k
views
8 follow
merge large amount of fastq files into a single one
ChIP-Seq fastq
updated 12 months ago by 39k • written 8.2 years ago by ▴ 220
106
votes
45
replies
81k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 8 months ago by ▴ 30 • written 10.8 years ago by ▴ 320
70
votes
20
replies
81k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl identifiers mapping
updated 4 months ago by 39k • written 12.5 years ago by ▴ 180
185
votes
43
replies
79k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 8 months ago by 39k • written 13.2 years ago by ★ 1.6k
120
votes
8
replies
78k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 16 months ago by 39k • written 8.7 years ago by ▴ 520
136
votes
25
replies
77k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 13 months ago by 39k • written 11.1 years ago by ★ 4.2k
33
votes
4
replies
77k
views
7 follow
Merging Bam Files
picard samtools
updated 4.0 years ago by ▴ 60 • written 11.4 years ago by ▴ 180
95
votes
27
replies
76k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 8 days ago by • 0 • written 11.0 years ago by ▴ 820
126
votes
24
replies
76k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence length fastq
updated 4.1 years ago by • 0 • written 10.0 years ago by ▴ 360
160
votes
62
replies
76k
views
37 follow
Selecting Random Pairs From Fastq?
random fastq sequence illumina code
updated 11 months ago by • 0 • written 12.2 years ago by 4.1k
99
votes
16
replies
75k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq coverage
8.5 years ago by Obi Griffith 20k
17
votes
12
replies
75k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast blastn sift makeblastdb
updated 9 months ago by • 0 • written 8.6 years ago by ▴ 320
82
votes
21
replies
74k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by ★ 3.0k • written 4.8 years ago by ▴ 540
103
votes
12
replies
73k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 7 months ago by 39k • written 11.6 years ago by ★ 1.7k
20
votes
2
replies
72k
views
Subsetting in R based on row name?
R
updated 7.1 years ago by 103k • written 7.1 years ago by ▴ 80
122
votes
17
replies
71k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 14 months ago by 39k • written 12.1 years ago by ▴ 370
43
votes
25
replies
70k
views
10 follow
Will A Masters In Bioinformatics Help Me In Getting A Job?
career education
updated 12.2 years ago by ★ 1.4k • written 12.2 years ago by ▴ 50
22
votes
2
replies
70k
views
How Can I Make A Bed File?
bed
updated 11.7 years ago by ▴ 260 • written 11.7 years ago by ▴ 580
67
votes
18
replies
70k
views
17 follow
Project For A Beginner Bioinformatics Student
project java
updated 10 months ago by 39k • written 11.5 years ago by ▴ 230
235
votes
45
replies
69k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen sequencing illumina exome human
updated 11.9 years ago by ▴ 50 • written 13.0 years ago by 4.9k
33
votes
17
replies
69k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray heatmap
updated 4 months ago by 39k • written 12.0 years ago by ▴ 80
59
votes
15
replies
69k
views
9 follow
BAM/SAM to FASTA conversion
sam bam
updated 13 months ago by 39k • written 8.3 years ago by ★ 1.4k
42
votes
14
replies
69k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 12 months ago by 39k • written 12.4 years ago by ▴ 250
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 4 months ago by 39k • written 10.7 years ago by 20k
188
votes
50
replies
68k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 8 months ago by 39k • written 12.6 years ago by ▴ 340
138
votes
21
replies
68k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer gene database oncogene tumor
2.6 years ago by Malachi Griffith 19k
54
votes
10
replies
68k
views
6 follow
Fold change - a final explanation
RNA-Seq
updated 2.7 years ago by • 0 • written 4.6 years ago by ▴ 320
24
votes
23
replies
67k
views
7 follow
Multiple Histograms In One Plot
r
updated 17 months ago by 39k • written 9.9 years ago by ★ 1.8k
1
vote
2
replies
67k
views
"SyntaxError: unexpected EOF while parsing " IN PYTHON 3.7
PYTHON
updated 2.2 years ago by 98k • written 3.1 years ago by • 0
51
votes
18
replies
66k
views
10 follow
Extract User Defined Region From An Fasta File
sequence fasta
updated 5.8 years ago by ▴ 30 • written 11.9 years ago by ▴ 290
19
votes
8
replies
66k
views
6 follow
Pheatmap Annotation
r heatmap
updated 7.8 years ago by ▴ 550 • written 10.2 years ago by ▴ 80
40
votes
15
replies
66k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix conversion entrez
updated 7 months ago by 39k • written 9.9 years ago by ▴ 140
74
votes
13
replies
65k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 6 months ago by 39k • written 9.5 years ago by ★ 1.2k
114
votes
25
replies
65k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 3 months ago by ▴ 10 • written 12.3 years ago by 154k
45
votes
14
replies
65k
views
10 follow
Tutorial: Using R in Conda
R
updated 10 weeks ago by 39k • written 2.9 years ago by ▴ 690
35
votes
9
replies
65k
views
8 follow
Minor allele frequency calculation
SNP next-gen
updated 12 months ago by 39k • written 8.5 years ago by ▴ 50
20
votes
15
replies
64k
views
12 follow
Python Script To Translate Rna Sequences To Protein Sequences
python biopython translation
updated 9.7 years ago by ▴ 50 • written 12.6 years ago by ▴ 70
51
votes
15
replies
64k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization software
updated 13 months ago by 39k • written 12.0 years ago by ▴ 70
50
votes
15
replies
63k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts sequence fastq
updated 3 months ago by 39k • written 11.9 years ago by ★ 1.7k
53
votes
4
replies
63k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence next-gen-sequencing
updated 7 months ago by 39k • written 8.5 years ago by ▴ 800
40
votes
7
replies
63k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r rna heatmap clustering gene
updated 11 months ago by 39k • written 11.6 years ago by ▴ 450
26
votes
10
replies
62k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 11 weeks ago by 39k • written 2.2 years ago by ★ 1.3k
25
votes
5
replies
61k
views
7 follow
Rpkm Calculation For Genes
rpkm rna-seq
updated 10.6 years ago by 13k • written 10.6 years ago by ▴ 270
8
votes
6
replies
61k
views
How To Calculate Coverage
fastq coverage
updated 9.4 years ago by ▴ 90 • written 9.4 years ago by ★ 1.2k
361
votes
57
replies
60k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 8 months ago by 85k • written 13.2 years ago by 98k
11
votes
9
replies
60k
views
7 follow
combining fasta files
windows fasta notepad
updated 6 months ago by • 0 • written 8.4 years ago by ▴ 30
1,000 results • Page 2 of 20
Recent Votes
Answer: extract all fasta sequence from db v5
Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, but the Max expression are near 20,000
Comment: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
Answer: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
A: extract dendrogram cluster from pheatmap
Answer: Counting intronic reads in bulk RNA-seq
Answer: IGV displays genomic coordinates in a 1-based system or 0-based?
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Recent Replies
Comment: DEgs RNAseq by Juan • 0
Dear Delaney Sullivan, thanks, finlly I did my analisys
Answer: ScRNA data by Dr William Klubinski ▴ 10
It seems like your single cell RNAseq data does not already contain the Cell Barcodes or Unique Molecular Identifiers in the standard way -…
Comment: Demultiplexing bam file by GenoMax 129k
> Part of the header of the bam file So perhaps there are more samples. https://www.biostars.org/u/21477/: `grep "SM*" header_of_bam`. Is…
Answer: extract all fasta sequence from db v5 by GenoMax 129k
If you need the fasta sequence download from NCBI here (146 GB zip compressed file) : https://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
Comment: ScRNA data by GenoMax 129k
Is this from a SRA dataset? If so it is possible that you can get the correct information in `DataAccess` tab. Provide the accession number…
Comment: extract all fasta sequence from db v5 by Pierre Lindenbaum 154k
is version 4 compatible with blast v5 ? try to use version 4....
Comment: Pre-processing for Agilent microarray data? by solarchan7 • 0
thank you!
Comment: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b by alwayshope ▴ 20
Thanks a lot! Very helpful detailed guidance! Appreciate it a lot!
Answer: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b by Dr William Klubinski ▴ 10
The values you are getting, with a third quartile of appx 10 and a max of appx 20,000, seem quite standard for RNA-Seq analysis. The RNA-se…
Comment: Demultiplexing bam file by Pierre Lindenbaum 154k
you don't talk about the size in your question
Comment: Demultiplexing bam file by hasani.iut6 ▴ 60
so why the size of bam file is 40 gig?
Comment: Demultiplexing bam file by Pierre Lindenbaum 154k
> I want to separate every sample I don't understand. In your header there is only one sample : "`13.02.1402_POOL2"`
Comment: Error while running Megahit by Mensur Dlakic ★ 23k
We can't even begin to guess what the problem was without an error message.
Comment: DEgs RNAseq by dsull ★ 4.2k
Is this single-cell RNAseq or non-single-cell RNAseq? For single-cell, you typically don't do standard "differential gene expression analy…
Comment: Counting intronic reads in bulk RNA-seq by dsull ★ 4.2k
Correct, and I agree -- reads lying fully within introns are usually not counted for either single-cell or bulk. Inclusion of introns in a…
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