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227
votes
11
answers
131k
views
108 follow
11
answers
Tools To Calculate Average Coverage For A Bam File?
bam coverage sequencing written 8.0 years ago by Biomed ♦ 4.4k • updated 5 months ago by WouterDeCoster ♦ 36k
186
votes
5
answers
128k
views
97 follow
5
answers
How To Filter Mapped Reads With Samtools
samtools written 6.2 years ago by sohadb1357 • 470 • updated 6 months ago by Simply Bioinformatics • 110
90
votes
5
answers
122k
views
39 follow
5
answers
What'S The Difference Between Cds And Orf?
cds orf written 6.6 years ago by shiy05 • 280 • updated 7 weeks ago by jazzyl5660 • 0
305
votes
10
answers
106k
views
154 follow
10
answers
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel tools next-gen ngs tool written 5.9 years ago by ole.tange • 3.3k • updated 8 months ago by suny.bio • 0
36
votes
3
answers
90k
views
28 follow
3
answers
How To Update R In Ubuntu ?
R ubuntu written 5.1 years ago by Arpitha Hebbar • 180 • updated 8 months ago by dexetra.in • 0
114
votes
20
answers
90k
views
59 follow
20
answers
Is There A Free Alternative To Ingenuity Pathway Analysis?
pathway network written 7.9 years ago by Gon • 440 • updated 10 months ago by Francis Crick • 50
19
votes
4
answers
81k
views
9 follow
4
answers
Calculating P-Values From Z-Scores
R statistics written 7.0 years ago by Diana • 750 • updated 3 months ago by Kevin Blighe ♦ 35k
191
votes
9
answers
76k
views
170 follow
9
answers
Tutorial: How to download raw sequence data from GEO/SRA
geo sra fastq tutorial download bam written 4.4 years ago by Obi Griffith ♦ 17k • updated 5 weeks ago by Renesh • 1.5k
98
votes
7
answers
76k
views
26 follow
7
answers
Correct Way To Parse A Fasta File In Python
fasta python parsing written 8.8 years ago by Eric Normandeau ♦ 10k • updated 4 months ago by RamRS ♦ 20k
148
votes
1
answer
74k
views
89 follow
1
answer
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
tool genome conversion coordinates ensembl liftover written 5.9 years ago by Malachi Griffith ♦ 17k
232
votes
25
answers
66k
views
58 follow
25
answers
Which Are The Best Programming Languages For A Bioinformatician?
subjective programming written 9.0 years ago by Giovanni M Dall'Olio ♦ 26k • updated 9 months ago by robert.branex • 0
32
votes
7
answers
56k
views
24 follow
7
answers
How To Draw A Heat Map For Gene Expression Data?
microarray heatmap written 7.6 years ago by Fahmida • 80 • updated 8 months ago by sonpham • 550
86
votes
6
answers
49k
views
34 follow
6
answers
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
merge picard samtools bam written 7.6 years ago by 2184687-1231-83- • 4.9k • updated 25 days ago by mmfansler • 260
51
votes
3
answers
49k
views
32 follow
3
answers
Extract Reads From A Bam File That Fall Within A Given Region
bam written 6.5 years ago by abi • 260 • updated 8 months ago by Alex Reynolds ♦ 27k
87
votes
4
answers
48k
views
26 follow
4
answers
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix written 6.1 years ago by lyz10302012 • 310 • updated 4 months ago by zx8754 ♦ 6.2k
63
votes
0
answers
48k
views
66 follow
0
answers
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
R tutorial classification cancer written 5.2 years ago by Nicholas Spies • 1.0k • updated 4 months ago by RamRS ♦ 20k
126
votes
9
answers
48k
views
66 follow
9
answers
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
splicing tools rna-seq alternative-splicing written 5.9 years ago by Nicolas Rosewick ♦ 7.2k • updated 9 months ago by kristoffer.vittingseerup • 1.3k
110
votes
9
answers
48k
views
63 follow
9
answers
Database Of Tumor Suppressors And/Or Oncogenes
gene database tumor oncogene cancer written 7.1 years ago by Malachi Griffith ♦ 17k • updated 6 weeks ago by 21angelicguitars • 0
72
votes
11
answers
47k
views
38 follow
11
answers
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta written 6.5 years ago by Mchimich • 250 • updated 9 months ago by Kzra • 10
168
votes
21
answers
47k
views
70 follow
21
answers
How To Remove The Same Sequences In The Fasta Files?
fasta duplicates sequence written 8.3 years ago by Zhangleisdau • 270 • updated 9 weeks ago by michau • 10
159
votes
2
answers
46k
views
157 follow
2
answers
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
tutorial tcga rna-seq survival written 3.5 years ago by TriS • 3.5k • updated 5 weeks ago by skjobs0123 • 0
54
votes
1
answer
45k
views
39 follow
1
answer
Number of mapped reads from BAM file
reads bam sam mapping written 3.8 years ago by Prakki Rama • 2.2k • updated 5 months ago by iraia.munoa • 50
51
votes
3
answers
45k
views
23 follow
3
answers
Convertion Of Gff3 To Gtf
gtf gff written 6.7 years ago by geek_y ♦ 8.8k • updated 8 months ago by Giuseppe • 0
52
votes
6
answers
43k
views
19 follow
6
answers
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
fasta next-gen sequencing perl R rna written 7.3 years ago by Hamilton • 260 • updated 7 months ago by har-wradim • 20
88
votes
14
answers
43k
views
32 follow
14
answers
Tool to generate proportional Venn Diagrams?
visualization written 7.8 years ago by Ryan D • 3.3k • updated 3 months ago by zx8754 ♦ 6.2k
128
votes
17
answers
42k
views
108 follow
17
answers
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial written 6.1 years ago by vijay • 1.4k • updated 5 months ago by MetaTK • 10
75
votes
6
answers
42k
views
47 follow
6
answers
How to plot coverage and depth statistics of a bam file
sequencing next-gen coverage bam depth written 4.6 years ago by krithika.gu • 250 • updated 6 months ago by Fred0730 • 40
178
votes
0
answers
42k
views
120 follow
0
answers
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
tutorial coordinates written 5.2 years ago by Obi Griffith ♦ 17k
116
votes
11
answers
38k
views
32 follow
11
answers
Multiline Fasta To Single Line Fasta
fasta sequence written 7.6 years ago by Palu • 170 • updated 12 months ago by teckpor • 10
124
votes
5
answers
37k
views
89 follow
5
answers
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
cancer tutorial tcga maf music mutation written 5.8 years ago by Cyriac Kandoth ♦ 5.2k • updated 11 months ago by Shicheng Guo • 7.3k
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