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15
votes
1
answer
6.3k
views
8 follow
1
answer
Deciphering Cigar
cigar next-gen samtools sam alignment written 7.8 years ago by Leszek ♦ 4.0k • updated 7 months ago by Biostar ♦♦ 20
4
votes
2
answers
1.2k
views
2
answers
CIGAR operations performed according to strand or to read?
sequencing read format sam cigar written 2.3 years ago by Macspider • 3.0k • updated 11 months ago by shouldsee.gem • 0
0
votes
0
answers
713
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 11 months ago by kiki4133 • 0
3
votes
0
answers
876
views
5 follow
0
answers
How to calculate percent identity from sam file?
assembly sam samtools mapping cigar written 12 months ago by O.rka • 170
2
votes
1
answer
474
views
1
answer
Filtering noise out of SAM file using CIGAR
cigar sam written 16 months ago by blur • 110 • updated 16 months ago by Carambakaracho • 2.0k
2
votes
1
answer
633
views
1
answer
Get sequences from a BAM file as strings spaced out as described by cigar
R alignment genomicalignments bam cigar written 17 months ago by yesitsjess • 0 • updated 17 months ago by Matt Shirley ♦ 9.3k
20
votes
2
answers
7.3k
views
5 follow
2
answers
Going From Cigar String In Sam To Genomic Coordinates?
cigar alignment sam parsing written 9.7 years ago by User 9996 • 810 • updated 19 months ago by RamRS ♦ 26k
3
votes
0
answers
872
views
0
answers
SAM CIGAR parsing and position counter in R
cigar parsing sam R written 23 months ago by niu.shengyong • 50
6
votes
2
answers
1.0k
views
2
answers
How to convert from a cigar string to extended cigar string?
extended cigar cigar c++ sam bam written 23 months ago by omariqbal2017 • 0 • updated 23 months ago by genomax ♦ 80k
10
votes
2
answers
1.3k
views
2
answers
When Hard clipping is used instead of the Soft clipping ?
clipping cigar hard clipping written 23 months ago by 2012secondseason • 20 • updated 23 months ago by Devon Ryan ♦ 94k
2
votes
1
answer
845
views
1
answer
In CIGAR table, what does P operation mean?
cigar silent deletion padding written 24 months ago by 2012secondseason • 20 • updated 24 months ago by Pierre Lindenbaum ♦ 127k
2
votes
3
answers
496
views
3
answers
What's the difference between 'clipping' and 'unmapped' and 'skipped'?
tablet alignment cigar written 2.0 years ago by 2012secondseason • 20 • updated 2.0 years ago by Zhixue • 10
4
votes
1
answer
537
views
1
answer
How can overlap with paired end sequence??
cigar paired end alignment tablet written 2.0 years ago by 2012secondseason • 20 • updated 2.0 years ago by d-cameron • 2.1k
3
votes
1
answer
886
views
1
answer
extract all the cigar sequences
cigar written 2.1 years ago by KVC_bioinfo • 410 • updated 2.1 years ago by cschu181 • 2.2k
3
votes
2
answers
2.2k
views
2
answers
Cigar And Md String Do Not Match In Bowtie 0.12.8
cigar bowtie written 7.5 years ago by jeremy • 80 • updated 2.2 years ago by Rubus Pi • 0
2
votes
0
answers
1.1k
views
0
answers
Getting genomic locations from cigar string
cigar python written 2.3 years ago by KVC_bioinfo • 410
4
votes
2
answers
1.5k
views
7 follow
2
answers
filter BAM file for reads that map 100% identity
cigar bam samtools written 2.3 years ago by oriolebaltimore • 130 • updated 2.3 years ago by h.mon ♦ 29k
9
votes
2
answers
8.0k
views
5 follow
2
answers
Extracting Reads Containing A Specific Variant From A Bam File
cigar format sam bam written 6.4 years ago by Nick Stoler • 70 • updated 2.5 years ago by Biostar ♦♦ 20
4
votes
1
answer
1.1k
views
1
answer
Mismatch on first base gives wrong TSS
cigar first-base mismatch clip-mismatch cage written 3.2 years ago by Chirag Nepal • 2.2k • updated 3.0 years ago by Charles Plessy • 2.7k
13
votes
2
answers
1.6k
views
7 follow
2
answers
How to convert extended CIGAR to regular CIGAR
cigar bam sam written 3.2 years ago by artemd • 10 • updated 3.2 years ago by Pierre Lindenbaum ♦ 127k
8
votes
1
answer
1.2k
views
1
answer
Splitting SAM/BAM alignments
cigar bam sam htslib written 3.4 years ago by Zev.Kronenberg ♦ 11k • updated 3.4 years ago by Pierre Lindenbaum ♦ 127k
0
votes
0
answers
749
views
0
answers
multiple Alignment Form
multiple alignment cigar alignment form written 3.4 years ago by midox • 260
9
votes
1
answer
8.8k
views
13 follow
1
answer
Samtools Filter Reads Cigar Field
cigar samtools written 6.6 years ago by dfernan • 670 • updated 3.9 years ago by Biostar ♦♦ 20
7
votes
1
answer
2.6k
views
1
answer
How does a skipped region from a CIGAR string (N) look in the alignment?
cigar alignment written 4.9 years ago by Niek De Klein • 2.5k • updated 4.9 years ago by Devon Ryan ♦ 94k
23
votes
2
answers
8.3k
views
6 follow
2
answers
In Cigar String, What Is The Difference Between 'N' And 'D' ?
cigar bam sam written 6.0 years ago by Chen • 970 • updated 4.9 years ago by amblina • 90
0
votes
1
answer
1.3k
views
1
answer
Using CIGAR match operators
cigar sam written 5.0 years ago by mikhail.shugay ♦ 3.4k • updated 5.0 years ago by Brian Bushnell ♦ 17k
5
votes
1
answer
3.1k
views
1
answer
CIGAR M operator maps off end of reference
exome cigar written 5.4 years ago by Chirag Nepal • 2.2k • updated 5.4 years ago by smilefreak • 420
32
votes
2
answers
5.2k
views
6 follow
2
answers
Is it possible to reconstruct alignment from CIGAR and MD strings alone?
cigar alignment rna-seq written 5.6 years ago by Lynxoid • 220 • updated 5.5 years ago by Istvan Albert ♦♦ 83k
2
votes
1
answer
3.1k
views
1
answer
Why "No real operator (M|I|D|N)" in picard?
cigar picard written 5.8 years ago by dariober ♦ 11k • updated 5.8 years ago by Pierre Lindenbaum ♦ 127k
0
votes
0
answers
1.4k
views
0
answers
Missing Cigar In Sam Output (Cushaw2)
cigar sam written 6.3 years ago by stolarek.ir • 640 • updated 5.8 years ago by Biostar ♦♦ 20
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