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1,000 results • Page 1 of 20
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226
votes
39
replies
281k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 7 months ago by 38k • written 13.4 years ago by ▴ 620
64
votes
3
replies
268k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein gene-expression RNA-Seq
updated 17 days ago by 38k • written 8.8 years ago by ▴ 960
267
votes
29
replies
251k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 4 months ago by 38k • written 10.4 years ago by ▴ 610
319
votes
90
replies
214k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 6 months ago by 38k • written 12.2 years ago by 4.8k
43
votes
24
replies
193k
views
25 follow
How To Update R In Ubuntu ?
r ubuntu
updated 11 months ago by ▴ 50 • written 9.3 years ago by ▴ 210
151
votes
42
replies
174k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 10 months ago by 38k • written 11.1 years ago by 20k
276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 10 months ago by 38k • written 8.6 years ago by 20k
188
votes
21
replies
163k
views
11 follow
Forward And Reverse Strand Conventions
sequence strand
updated 4 months ago by 97k • written 12.4 years ago by ★ 2.8k
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
158
votes
8
replies
150k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix
updated 8 months ago by 38k • written 10.3 years ago by ▴ 430
358
votes
79
replies
136k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 4 months ago by 38k • written 10.1 years ago by ★ 4.3k
223
votes
38
replies
134k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 3 months ago by ▴ 90 • written 10.1 years ago by 19k
90
votes
38
replies
128k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 months ago by ▴ 10 • written 10.7 years ago by ▴ 370
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
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 12.0 years ago by ▴ 530
23
votes
9
replies
121k
views
8 follow
How to calculate "fold changes" in gene expression?
R gene
updated 6 weeks ago by 38k • written 7.9 years ago by ▴ 70
26
votes
10
replies
120k
views
Calculating P-Values From Z-Scores
statistics r
updated 9 months ago by 38k • written 11.1 years ago by ▴ 900
13
votes
8
replies
118k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 5 months ago by 38k • written 11.4 years ago by ▴ 500
97
votes
9
replies
113k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 11 months ago by ▴ 40 • written 9.5 years ago by ▴ 750
46
votes
10
replies
112k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm rpkm rna-seq
updated 3 months ago by 38k • written 10.0 years ago by ★ 1.5k
729
votes
161
replies
108k
views
100 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 9 days ago by 1.6k • written 6.3 years ago by 97k
73
votes
25
replies
97k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 8 months ago by 38k • written 7.9 years ago by ▴ 250
100
votes
15
replies
97k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 19 days ago by ▴ 20 • written 10.8 years ago by 12k
59
votes
9
replies
94k
views
10 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression RNA-Seq
updated 6 weeks ago by 38k • written 5.5 years ago by ★ 2.1k
274
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 22 days ago by 38k • written 9.4 years ago by 20k
118
votes
53
replies
87k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 4 days ago by • 0 • written 8.8 years ago by ▴ 330
97
votes
19
replies
87k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 7 months ago by 38k • written 13.1 years ago by 27k
70
votes
16
replies
85k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna samtools mouse
updated 11 months ago by 153k • written 11.5 years ago by ▴ 510
167
votes
41
replies
85k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence fasta
updated 7 weeks ago by • 0 • written 11.8 years ago by ▴ 240
238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.6 years ago by ★ 4.6k
84
votes
16
replies
84k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 4 months ago by ▴ 50 • written 7.9 years ago by ★ 2.6k
99
votes
31
replies
81k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 8 months ago by 38k • written 11.7 years ago by ★ 5.0k
79
votes
22
replies
81k
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 4 months ago by 38k • written 11.4 years ago by ▴ 290
106
votes
45
replies
80k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 6 months ago by ▴ 20 • written 10.7 years ago by ▴ 320
70
votes
20
replies
80k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl identifiers mapping
updated 10 weeks ago by 38k • written 12.4 years ago by ▴ 180
55
votes
11
replies
79k
views
8 follow
merge large amount of fastq files into a single one
ChIP-Seq fastq
updated 9 months ago by 38k • written 8.0 years ago by ▴ 220
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 6 months ago by 38k • written 13.0 years ago by ★ 1.6k
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
157
votes
62
replies
74k
views
37 follow
Selecting Random Pairs From Fastq?
random fastq sequence illumina code
updated 9 months ago by • 0 • written 12.0 years ago by 4.1k
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 10 days ago by 2.6k • written 10.8 years ago by ▴ 820
15
votes
12
replies
73k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast blastn sift makeblastdb
updated 7 months ago by • 0 • written 8.4 years ago by ▴ 310
103
votes
12
replies
71k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 5 months ago by 38k • written 11.4 years ago by ★ 1.7k
81
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 530
67
votes
18
replies
69k
views
17 follow
Project For A Beginner Bioinformatics Student
project java
updated 8 months ago by 38k • written 11.4 years ago by ▴ 230
33
votes
17
replies
69k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray heatmap
updated 9 weeks ago by 38k • written 11.8 years ago by ▴ 80
40
votes
14
replies
68k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 10 months ago by 38k • written 12.2 years ago by ▴ 250
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 weeks ago by 38k • written 10.5 years ago by 20k
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 5 months ago by 38k • written 12.4 years ago by ▴ 340
59
votes
15
replies
67k
views
9 follow
BAM/SAM to FASTA conversion
sam bam
updated 11 months ago by 38k • written 8.1 years ago by ★ 1.4k
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 4 months ago by 38k • written 9.3 years ago by ★ 1.2k
1,000 results • Page 1 of 20
Recent Votes
Comment: bioinformatics problems solved by graphs data structure
Comment: bioinformatics problems solved by graphs data structure
Answer: How to analize multiple letters codes in COG IDs?
Answer: PCA in gene expression
Answer: PCA in gene expression
Comment: Enrichment analysis based on kegg for zebrafish
Question on number of possible alignments
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Commentator to colindaven 4.6k
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Recent Replies
Comment: bioinformatics problems solved by graphs data structure by lieven.sterck 14k
et mon français est assez bien pour comprendre ce que tu as écrit la ;-)
Comment: How to analize multiple letters codes in COG IDs? by Constanza • 0
Thanks for answering so fast, it was very helpful. I shouldn't pay much attention to if COGs are separated by a comma or not then. As long…
Comment: bioinformatics problems solved by graphs data structure by lieven.sterck 14k
well, because this is not you guys' private forum, there are other people participating (not native french speaking) , just to give a reaso…
Answer: How to get gene from PSIBLAST resuts by lieven.sterck 14k
what you likely will need to do: 1. get the ID of the protein that you are interested in (out of result from PSIBLAST) 2. lookup that ID…
Answer: How to analize multiple letters codes in COG IDs? by Mensur Dlakic ★ 23k
The meaning of individual letters is described in a well-known COG functional code: https://ecoliwiki.org/colipedia/index.php/Clusters_o…
Comment: How to find promoter sequence of a gene? by sunyeping ▴ 40
The organism is mice.
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file? by Pierre Lindenbaum 153k
BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gperte…
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs? by Darked89 4.2k
You may try to check what happened with DEGs obtained using the 300 fragments assembly by getting the sequences of these genes and comparin…
Comment: ExomeDepth installation error by Medha • 0
Thanks, that did work. Also in next steps, there are some arguments like bam.files, I was wondering do we require to have multiple bam fil…
Comment: ExomeDepth installation error by jared.andrews07 ★ 14k
No idea, I don't use databricks. I'd read the docs, find a local expert to help you out, or contact their support, likely in that order.
Comment: ExomeDepth installation error by Medha • 0
Hi @jaredandrews07 thanks for reverting back. I am new to R and just want to make sure ExomeDepth is working for the first time. For the Rs…
Comment: Embedded stop codon in translated nucleotide sequences in DAMBE by Mensur Dlakic ★ 23k
It is not obvious to me what exact steps you did here, but here is what I do know: there will always be stop codons even in open reading fr…
Comment: Error with a function in ATAC-seq analysis by Chris ▴ 70
So you skip the GRanges()? Yes, no error anymore but I am not sure if that causes changing in downstream analysis.
Answer: ClusterProfiler enrichKEGG – remove organism name in plots? by jv ★ 1.0k
`stringr::str_remove` can remove " - Mus musculus (house mouse)" from the pathway names which are stored under `KEGGPATHID2NAME$to` in your…
Comment: Error with a function in ATAC-seq analysis by jv ★ 1.0k
run `union` on the data frames
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