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105
votes
8
answers
39k
views
50 follow
8
answers
Workflow Or Tutorial For Snp Calling?
alignment next-gen samtools snp sequencing written 8.3 years ago by Matthieu • 430 • updated 3.4 years ago by alexisdereeper • 30
55
votes
6
answers
38k
views
29 follow
6
answers
Estimate Insert Size In Paired-End/Mate-Pair
next-gen paired alignment sequencing written 7.6 years ago by Ric • 140 • updated 7.6 years ago by Ketil ♦ 4.0k
94
votes
15
answers
31k
views
28 follow
15
answers
What Is The Quickest Algorithm For Range Overlap?
python database next-gen alignment sequencing written 9.0 years ago by User 1586 • 280 • updated 15 months ago by endrebak • 780
75
votes
5
answers
25k
views
27 follow
5
answers
Star Or Tophat?
rnaseq tophat alignment written 5.6 years ago by lkmklsmn • 890 • updated 5.3 years ago by super • 60
39
votes
5
answers
25k
views
25 follow
5
answers
How to extract unique mapped results from Bowtie2 bam results?
alignment written 5.2 years ago by zhwjmch • 90 • updated 3.2 years ago by merodev • 140
37
votes
3
answers
2.4k
views
25 follow
3
answers
Tutorial: Which human reference genome should I use?
genome assembly tutorial alignment written 10 months ago by finswimmer ♦ 12k
72
votes
5
answers
12k
views
22 follow
5
answers
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment tutorial bwa written 6.5 years ago by lh3 ♦ 31k • updated 6.4 years ago by pan.alexiou • 10
34
votes
1
answer
12k
views
18 follow
1
answer
bash loop for alignment RNA-seq data
next-gen alignment rna-seq written 5.3 years ago by Paul • 1.3k • updated 21 months ago by parmarsachinsingh • 0
17
votes
2
answers
4.0k
views
18 follow
2
answers
Best tool for variant calling
genome alignment next-gen snp written 15 months ago by williamsbrian5064 • 170 • updated 9 months ago by claire • 0
68
votes
5
answers
8.9k
views
16 follow
5
answers
What Should I Use Blat For?
alignment written 6.7 years ago by KCC • 3.9k • updated 6.7 years ago by David Quigley ♦ 11k
36
votes
7
answers
1.3k
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 21 months ago by dhbradshaw • 130 • updated 21 months ago by Puli Chandramouli Reddy • 180
18
votes
1
answer
641
views
16 follow
1
answer
Forum: Review of the CIGAR string format
forum alignment written 9 months ago by Juke-34 • 2.4k
55
votes
1
answer
2.1k
views
16 follow
1
answer
Forum: Best RNA-Seq aligner: A comparison of mapping tools
genome forum ngs alignment rna-seq sequence written 6 months ago by David Langenberger ♦ 9.0k
32
votes
3
answers
7.6k
views
15 follow
3
answers
Which Aligners Recognize Soft-Masked Repeats In Reference Sequences?
alignment written 8.8 years ago by Jeremy Leipzig ♦ 18k • updated 6.4 years ago by Ali R. Vahdati • 190
38
votes
6
answers
8.0k
views
14 follow
6
answers
Multiple Sequence Alignment For Cdnas
alignment cdna clustalw multiple written 8.9 years ago by Haibao Tang ♦ 3.0k • updated 3.3 years ago by kissaj • 90
15
votes
6
answers
6.3k
views
14 follow
6
answers
A Question About The Sam Entry For A Query Aligned To Multiple Places
format alignment sam bowtie multiple written 7.4 years ago by Tianyang Li • 490 • updated 7.4 years ago by Xianjun • 250
27
votes
1
answer
4.7k
views
14 follow
1
answer
Grch38 And Reference Alignment
alignment human written 5.5 years ago by aniketd86 • 150 • updated 5.5 years ago by deanna.church • 1.1k
37
votes
8
answers
3.8k
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 9.3 years ago by Jeremy Leipzig ♦ 18k • updated 11 months ago by RamRS ♦ 23k
19
votes
2
answers
8.2k
views
13 follow
2
answers
When Aligning Mirna (Micro Rna) What Reference Is Better? (Whole Genome Or Mirbase)
alignment reference mirna written 8.8 years ago by Doctoroots • 780 • updated 2.5 years ago by enxxx23 • 230
33
votes
5
answers
6.0k
views
13 follow
5
answers
Should I Strip Alignment Columns Before Making A Tree?
phylogenetics alignment tree written 8.4 years ago by John • 770 • updated 6.0 years ago by Biostar ♦♦ 20
16
votes
2
answers
5.1k
views
13 follow
2
answers
How Do I Align More Than Five Long Dna Scaffolds (Contigs) To The Reference Gene?
pairwise alignment reference written 5.6 years ago by biostar • 150 • updated 3.9 years ago by Darked89 ♦ 4.2k
10
votes
5
answers
11k
views
13 follow
5
answers
Finding a sequence in a fasta file
sequence alignment written 5.2 years ago by mbk0asis • 460 • updated 5.2 years ago by PoGibas ♦ 4.8k
37
votes
6
answers
6.7k
views
12 follow
6
answers
Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads
splicing alignment rna written 9.1 years ago by Wjeck • 480 • updated 8.8 years ago by Zee • 40
32
votes
3
answers
8.5k
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 9.0 years ago by Colin • 120 • updated 9.0 years ago by jvijai • 1.1k
22
votes
3
answers
10k
views
12 follow
3
answers
Long read alignment
alignment rna-seq written 4.8 years ago by bdeonovic • 180 • updated 4.8 years ago by lh3 ♦ 31k
64
votes
2
answers
6.7k
views
12 follow
2
answers
Alignment and mapping
alignment next-gen mapping written 3.4 years ago by statfa • 450 • updated 3.4 years ago by Benn ♦ 7.4k
38
votes
2
answers
6.0k
views
12 follow
2
answers
Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score does not seem to do the trick in my case)
next-gen alignment bwa written 2.2 years ago by betsy.s.collins • 110 • updated 2.2 years ago by John ♦ 12k
15
votes
0
answers
4.3k
views
12 follow
0
answers
STAR align multiple files
alignment chip-seq star rna-seq written 22 months ago by ta_awwad • 220 • updated 16 months ago by Bog • 20
38
votes
6
answers
11k
views
11 follow
6
answers
Pairwise Genome Alignment
pairwise genome alignment written 8.8 years ago by Andrea_Bio • 2.5k • updated 8.0 years ago by Larry_Parnell ♦ 16k
22
votes
5
answers
9.4k
views
11 follow
5
answers
Bam : Extract Only Alignment With A Specific Length
alignment extraction length rna bam written 7.9 years ago by Nicolas Rosewick ♦ 8.0k • updated 7.9 years ago by Marvin • 850
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