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<prev • 43 results • page 1 of 2 • next >
14
votes
1
answer
5.8k
views
8 follow
1
answer
Deciphering Cigar
cigar next-gen samtools sam alignment written 7.1 years ago by Leszek ♦ 4.0k • updated 16 days ago by Biostar ♦♦ 20
4
votes
2
answers
856
views
2
answers
CIGAR operations performed according to strand or to read?
sequencing read format sam cigar written 20 months ago by Macspider • 2.9k • updated 3 months ago by shouldsee.gem • 0
0
votes
0
answers
320
views
0
answers
Extracting CIGAR string from a specific region of a read in a bam file using pysam?
cigar bam pysam rna-seq written 4 months ago by kiki4133 • 0
3
votes
0
answers
472
views
5 follow
0
answers
How to calculate percent identity from sam file?
assembly sam samtools mapping cigar written 5 months ago by O.rka • 110
2
votes
1
answer
327
views
1
answer
Filtering noise out of SAM file using CIGAR
cigar sam written 9 months ago by blur • 110 • updated 9 months ago by Carambakaracho • 1.5k
2
votes
1
answer
445
views
1
answer
Get sequences from a BAM file as strings spaced out as described by cigar
R alignment genomicalignments bam cigar written 9 months ago by yesitsjess • 0 • updated 9 months ago by Matt Shirley ♦ 9.1k
19
votes
2
answers
6.9k
views
5 follow
2
answers
Going From Cigar String In Sam To Genomic Coordinates?
cigar alignment sam parsing written 9.1 years ago by User 9996 • 800 • updated 11 months ago by RamRS ♦ 23k
3
votes
0
answers
594
views
0
answers
SAM CIGAR parsing and position counter in R
cigar parsing sam R written 15 months ago by niu.shengyong • 40
6
votes
2
answers
761
views
2
answers
How to convert from a cigar string to extended cigar string?
extended cigar cigar c++ sam bam written 16 months ago by omariqbal2017 • 0 • updated 16 months ago by genomax ♦ 70k
8
votes
2
answers
853
views
2
answers
When Hard clipping is used instead of the Soft clipping ?
clipping cigar hard clipping written 16 months ago by 2012secondseason • 20 • updated 16 months ago by Devon Ryan ♦ 91k
2
votes
1
answer
564
views
1
answer
In CIGAR table, what does P operation mean?
cigar silent deletion padding written 16 months ago by 2012secondseason • 20 • updated 16 months ago by Pierre Lindenbaum ♦ 122k
2
votes
3
answers
376
views
3
answers
What's the difference between 'clipping' and 'unmapped' and 'skipped'?
tablet alignment cigar written 17 months ago by 2012secondseason • 20 • updated 17 months ago by Zhixue • 10
4
votes
1
answer
412
views
1
answer
How can overlap with paired end sequence??
cigar paired end alignment tablet written 17 months ago by 2012secondseason • 20 • updated 17 months ago by d-cameron • 2.1k
3
votes
1
answer
630
views
1
answer
extract all the cigar sequences
cigar written 18 months ago by KVC_bioinfo • 400 • updated 18 months ago by cschu181 • 1.7k
3
votes
2
answers
2.1k
views
2
answers
Cigar And Md String Do Not Match In Bowtie 0.12.8
cigar bowtie written 6.9 years ago by jeremy • 80 • updated 19 months ago by Rubus Pi • 0
2
votes
0
answers
822
views
0
answers
Getting genomic locations from cigar string
cigar python written 20 months ago by KVC_bioinfo • 400
4
votes
2
answers
1.1k
views
7 follow
2
answers
filter BAM file for reads that map 100% identity
cigar bam samtools written 21 months ago by oriolebaltimore • 110 • updated 21 months ago by h.mon ♦ 27k
8
votes
2
answers
7.3k
views
5 follow
2
answers
Extracting Reads Containing A Specific Variant From A Bam File
cigar format sam bam written 5.8 years ago by Nick Stoler • 70 • updated 22 months ago by Biostar ♦♦ 20
4
votes
1
answer
1.0k
views
1
answer
Mismatch on first base gives wrong TSS
cigar first-base mismatch clip-mismatch cage written 2.6 years ago by Chirag Nepal • 2.2k • updated 2.3 years ago by Charles Plessy • 2.7k
13
votes
2
answers
1.3k
views
7 follow
2
answers
How to convert extended CIGAR to regular CIGAR
cigar bam sam written 2.6 years ago by artemd • 10 • updated 2.6 years ago by Pierre Lindenbaum ♦ 122k
8
votes
1
answer
1.1k
views
1
answer
Splitting SAM/BAM alignments
cigar bam sam htslib written 2.8 years ago by Zev.Kronenberg ♦ 11k • updated 2.8 years ago by Pierre Lindenbaum ♦ 122k
0
votes
0
answers
652
views
0
answers
multiple Alignment Form
multiple alignment cigar alignment form written 2.8 years ago by midox • 230
8
votes
1
answer
8.1k
views
11 follow
1
answer
Samtools Filter Reads Cigar Field
cigar samtools written 6.0 years ago by dfernan • 650 • updated 3.3 years ago by Biostar ♦♦ 20
7
votes
1
answer
2.4k
views
1
answer
How does a skipped region from a CIGAR string (N) look in the alignment?
cigar alignment written 4.2 years ago by Niek De Klein • 2.5k • updated 4.2 years ago by Devon Ryan ♦ 91k
20
votes
2
answers
7.3k
views
6 follow
2
answers
In Cigar String, What Is The Difference Between 'N' And 'D' ?
cigar bam sam written 5.4 years ago by Chen • 900 • updated 4.3 years ago by amblina • 80
0
votes
1
answer
1.2k
views
1
answer
Using CIGAR match operators
cigar sam written 4.4 years ago by mikhail.shugay ♦ 3.3k • updated 4.4 years ago by Brian Bushnell ♦ 16k
5
votes
1
answer
2.8k
views
1
answer
CIGAR M operator maps off end of reference
exome cigar written 4.8 years ago by Chirag Nepal • 2.2k • updated 4.8 years ago by smilefreak • 420
32
votes
2
answers
4.9k
views
6 follow
2
answers
Is it possible to reconstruct alignment from CIGAR and MD strings alone?
cigar alignment rna-seq written 5.0 years ago by Lynxoid • 220 • updated 4.9 years ago by Istvan Albert ♦♦ 81k
2
votes
1
answer
2.9k
views
1
answer
Why "No real operator (M|I|D|N)" in picard?
cigar picard written 5.2 years ago by dariober ♦ 10k • updated 5.2 years ago by Pierre Lindenbaum ♦ 122k
0
votes
0
answers
1.2k
views
0
answers
Missing Cigar In Sam Output (Cushaw2)
cigar sam written 5.7 years ago by stolarek.ir • 600 • updated 5.2 years ago by Biostar ♦♦ 20
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