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109
votes
8
answers
41k
views
54 follow
8
answers
Workflow Or Tutorial For Snp Calling?
alignment next-gen samtools snp sequencing written 9.7 years ago by Matthieu • 460 • updated 4.9 years ago by alexisdereeper • 30
50
votes
3
answers
6.2k
views
38 follow
3
answers
Tutorial: Which human reference genome should I use?
genome assembly tutorial alignment written 2.3 years ago by finswimmer ♦ 14k
57
votes
6
answers
43k
views
32 follow
6
answers
Estimate Insert Size In Paired-End/Mate-Pair
next-gen paired alignment sequencing written 9.0 years ago by Ric • 170 • updated 9.0 years ago by Ketil ♦ 4.0k
48
votes
5
answers
30k
views
32 follow
5
answers
How to extract unique mapped results from Bowtie2 bam results?
alignment written 6.7 years ago by zhwjmch • 120 • updated 4.7 years ago by merodev • 140
30
votes
2
answers
7.7k
views
32 follow
2
answers
Best tool for variant calling
genome alignment next-gen snp written 2.7 years ago by williamsbrian5064 • 300 • updated 2.2 years ago by claire • 0
77
votes
3
answers
7.4k
views
31 follow
3
answers
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
R next-gen alignment rna-seq assembly written 16 months ago by Wox • 420
94
votes
15
answers
33k
views
28 follow
15
answers
What Is The Quickest Algorithm For Range Overlap?
python database next-gen alignment sequencing written 10.4 years ago by User 1586 • 280 • updated 2.7 years ago by endrebak • 840
77
votes
5
answers
28k
views
28 follow
5
answers
Star Or Tophat?
rnaseq tophat alignment written 7.0 years ago by lkmklsmn • 930 • updated 6.8 years ago by super • 60
72
votes
5
answers
13k
views
22 follow
5
answers
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment tutorial bwa written 8.0 years ago by lh3 ♦ 32k • updated 7.8 years ago by pan.alexiou • 10
89
votes
2
answers
11k
views
20 follow
2
answers
Alignment and mapping
alignment next-gen mapping written 4.9 years ago by statfa • 540 • updated 4.9 years ago by Benn ♦ 8.1k
35
votes
1
answer
16k
views
18 follow
1
answer
bash loop for alignment RNA-seq data
next-gen alignment rna-seq written 6.8 years ago by Paul • 1.4k • updated 3.2 years ago by parmarsachinsingh • 0
68
votes
5
answers
10.0k
views
16 follow
5
answers
What Should I Use Blat For?
alignment written 8.2 years ago by KCC • 4.0k • updated 8.2 years ago by David Quigley ♦ 11k
19
votes
0
answers
9.2k
views
16 follow
0
answers
STAR align multiple files
alignment chip-seq star rna-seq written 3.3 years ago by ta_awwad • 300 • updated 2.8 years ago by Bog • 20
36
votes
7
answers
1.6k
views
16 follow
7
answers
Forum: Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
next-gen forum sequencing alignment rna-seq blast written 3.2 years ago by dhbradshaw • 130 • updated 3.2 years ago by Puli Chandramouli Reddy • 190
16
votes
2
answers
6.3k
views
16 follow
2
answers
bwa mem and multiply mapped reads
alignment bwa repetitive genome written 2.9 years ago by lfreeborn • 20 • updated 11 weeks ago by Biostar ♦♦ 20
18
votes
1
answer
1.7k
views
16 follow
1
answer
Forum: Review of the CIGAR string format
forum alignment written 2.3 years ago by Juke34 • 5.0k
55
votes
1
answer
7.7k
views
16 follow
1
answer
Forum: Best RNA-Seq aligner: A comparison of mapping tools
genome forum ngs alignment rna-seq sequence written 2.0 years ago by David Langenberger ♦ 9.5k
32
votes
3
answers
9.0k
views
15 follow
3
answers
Which Aligners Recognize Soft-Masked Repeats In Reference Sequences?
alignment written 10.3 years ago by Jeremy Leipzig ♦ 19k • updated 7.8 years ago by Ali R. Vahdati • 190
22
votes
2
answers
9.8k
views
15 follow
2
answers
When Aligning Mirna (Micro Rna) What Reference Is Better? (Whole Genome Or Mirbase)
alignment reference mirna written 10.2 years ago by Doctoroots • 790 • updated 4.0 years ago by enxxx23 • 240
12
votes
5
answers
14k
views
15 follow
5
answers
Finding a sequence in a fasta file
sequence alignment written 6.7 years ago by mbk0asis • 590 • updated 6.7 years ago by PoGibas ♦ 4.8k
38
votes
6
answers
9.3k
views
14 follow
6
answers
Multiple Sequence Alignment For Cdnas
alignment cdna clustalw multiple written 10.4 years ago by Haibao Tang ♦ 3.0k • updated 4.7 years ago by kissaj • 100
15
votes
6
answers
7.1k
views
14 follow
6
answers
A Question About The Sam Entry For A Query Aligned To Multiple Places
format alignment sam bowtie multiple written 8.9 years ago by Tianyang Li • 490 • updated 8.8 years ago by Xianjun • 280
13
votes
3
answers
14k
views
14 follow
3
answers
How To Use Coordinates In Order To Extract Sequences In Fasta File?
genome fasta alignment written 7.4 years ago by srpatel144 • 30 • updated 5.3 years ago by syxbestmayer • 10
27
votes
1
answer
5.3k
views
14 follow
1
answer
Grch38 And Reference Alignment
alignment human written 6.9 years ago by aniketd86 • 150 • updated 6.9 years ago by deanna.church • 1.1k
24
votes
1
answer
5.6k
views
14 follow
1
answer
Genotyping, genotype calling or SNP calling?
alignment snp written 3.3 years ago by James Reeve • 100 • updated 3.3 years ago by Kevin Blighe ♦ 69k
37
votes
8
answers
4.3k
views
13 follow
8
answers
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
alignment code programming written 10.8 years ago by Jeremy Leipzig ♦ 19k • updated 2.4 years ago by _r_am ♦ 32k
33
votes
5
answers
6.7k
views
13 follow
5
answers
Should I Strip Alignment Columns Before Making A Tree?
phylogenetics alignment tree written 9.9 years ago by John • 770 • updated 7.4 years ago by Biostar ♦♦ 20
16
votes
2
answers
5.8k
views
13 follow
2
answers
How Do I Align More Than Five Long Dna Scaffolds (Contigs) To The Reference Gene?
pairwise alignment reference written 7.0 years ago by biostar • 150 • updated 5.4 years ago by Darked89 ♦ 4.2k
37
votes
6
answers
7.1k
views
12 follow
6
answers
Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
splicing alignment rna written 10.6 years ago by Wjeck • 480 • updated 10.3 years ago by Zee • 40
32
votes
3
answers
9.3k
views
12 follow
3
answers
Any Hardware Recommendations For A Molecular Biology Lab That'S Getting Into Bioinformatics?
next-gen cloud chip-seq sequencing alignment hardware written 10.4 years ago by Colin • 120 • updated 10.4 years ago by jvijai • 1.2k
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