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Showing top results for tag: sam • reset
0
votes
1
reply
109
views
Can a read be aligned more than once?
alignment gaf read sam
updated 8 hours ago by 146k • written 10 hours ago by ▴ 40
4
votes
2
replies
261
views
Converting bam to sam using htslib C++ api
bam htslib sam
updated 4 weeks ago by 164k • written 4 weeks ago by ▴ 40
4
votes
1
reply
254
views
Extract bam file to sam inside code?
bam sam
updated 4 weeks ago by 164k • written 4 weeks ago by ▴ 40
3
votes
2
replies
338
views
Difference between gam and sam/bam files?
bam pangenome gam sam
4 weeks ago by Uveyik ▴ 40
1
vote
1
reply
312
views
When to use Sam Sort on a Bam file?
Sam Bam Sort File Collate
updated 3 months ago by 164k • written 3 months ago by ▴ 10
0
votes
1
reply
301
views
Difference between samtools stats insert size and TLEN in SAM/BAM file.
samtools insert-size SAM
updated 3 months ago by 44k • written 3 months ago by • 0
0
votes
3
replies
501
views
Sam file Header problem
Sam Header problem file
updated 5 months ago by 164k • written 5 months ago by • 0
1
vote
3
replies
799
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
5 months ago by kalavattam ▴ 270
0
votes
3
replies
496
views
Difference between samtools "-f 9" and "-f 11"
samtools sam bam
updated 6 months ago by 101k • written 6 months ago by • 0
4
votes
2
replies
2.4k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF SAM BAM GFF minimap2
updated 6 months ago by ▴ 130 • written 18 months ago by • 0
1
vote
1
reply
401
views
How do I get the 3bp sequence on either side of a co-ordinate
SAM genomics sequencing
updated 6 months ago by 44k • written 6 months ago by • 0
0
votes
1
reply
302
views
BRIG coverage.graph issues
BRIG sam
updated 7 months ago by 164k • written 7 months ago by ▴ 10
2
votes
5
replies
962
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 6 months ago by 44k • written 7 months ago by • 0
7
votes
5
replies
3.6k
views
What is chr EBV in human sam file?
SAM Bowtie2
written 6.3 years ago by ▴ 550
2
votes
1
reply
734
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated 11 months ago by 13k • written 11 months ago by ▴ 740
1
vote
7
replies
1.2k
views
Samtools filtering based on PNEXT
CRAM filtering samtools SAM BAM
updated 12 months ago by 101k • written 12 months ago by ★ 2.0k
1
vote
1
reply
730
views
Filtering for primary and secondary reads using sam flags (0 properly paired reads in alignment step)
freebayes samtools samflags sam paired-end
updated 12 months ago by ▴ 340 • written 12 months ago by ▴ 10
1
vote
4
replies
1.7k
views
bowtie mismatch 0 alignment output
sequencing bam sam bowtie rna-seq
updated 12 months ago by • 0 • written 3.4 years ago by ▴ 10
0
votes
1
reply
400
views
Does GATK SetNmMdAndUqTags reduces the size of a CRAM?
CRAM WGS sam GATK SetNmMdAndUqTags
updated 12 months ago by 164k • written 12 months ago by • 0
4
votes
6
replies
2.4k
views
6 follow
How to discard alignments from SAM/BAM file that have mismatches
BAM SAM minimap nanopore
updated 12 months ago by 20k • written 16 months ago by ▴ 50
5
votes
12
replies
1.7k
views
sam format in the emboss water program
emboss alignment sam water
updated 12 months ago by 3.1k • written 12 months ago by ★ 1.5k
2
votes
3
replies
787
views
Finding exactly where reads map from SAM
alignment read Bowtie SAM BWA
updated 12 months ago by 101k • written 12 months ago by • 0
1
vote
1
reply
510
views
Bam sort merge error?
bam linux sam
updated 13 months ago by 164k • written 13 months ago by • 0
7
votes
4
replies
896
views
BAM file read stats (A/T/C/G/ins/del) for each base position
SAM BAM Nanopore JBrowse
updated 14 months ago by ★ 1.9k • written 14 months ago by ▴ 20
5
votes
8
replies
4.5k
views
Distinguish between forward strand, plus strand, sense strand
pysam strand star sam
updated 14 months ago by • 0 • written 2.3 years ago by ▴ 40
0
votes
1
reply
486
views
How to get MD tag sequence of a read from a sam file given a bed file?
samtools bed sam cigar
updated 14 months ago by ▴ 340 • written 14 months ago by • 0
0
votes
2
replies
751
views
How to build a tree from SAM files?
SAM phylogeny alignment
14 months ago by Alina • 0
2
votes
5
replies
887
views
Help with htseq -count read counts
sam gtf RNA-seq htseq
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
2
votes
2
replies
703
views
Are SAM attributes necessary if I only keep the BAM files using STAR?
BAM SAM RNA-seq STAR
updated 15 months ago by 146k • written 15 months ago by ▴ 40
4
votes
5
replies
904
views
Samtools sort error: [pretty_header] invalid header
sam RNA-seq bam samtools
updated 16 months ago by 44k • written 16 months ago by ▴ 100
2
votes
2
replies
663
views
Identify similarly mapped reads in BAM/SAM?
bam igv sam python r
16 months ago by Eliveri ▴ 350
5
votes
5
replies
5.1k
views
Decoding MM and ML tags in .SAM file
samtools Methylation SAM
updated 10 months ago by ▴ 10 • written 17 months ago by ▴ 10
0
votes
6
replies
3.4k
views
How to extract alignments with 0 mismatch from sam or bam file by using samtools?
bam samtools sam
updated 17 months ago by • 0 • written 3.4 years ago by • 0
0
votes
0
replies
909
views
Invalid Contig error when using bamfile.fetch
sam Pysam bam python
18 months ago by bxxxmxxxx ▴ 10
3
votes
3
replies
2.0k
views
base modifications tags in SAM file
methylation SAM tag nanopore bam
updated 4 months ago by 6.8k • written 18 months ago by ▴ 20
1
vote
3
replies
928
views
".sam" file - should it contain multiple samples?
SAM
updated 18 months ago by 146k • written 18 months ago by ▴ 20
3
votes
6
replies
1.7k
views
bam index chromosome size limit
bam sam mapping rna-seq
updated 15 months ago by • 0 • written 19 months ago by • 0
3
votes
4
replies
993
views
How to filter bam file for only reads that span certain regions of the genome?
reference-genome bam sam bedtools
updated 19 months ago by 44k • written 19 months ago by • 0
0
votes
2
replies
828
views
Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage?
bamCoverage BAM SAM deeptools
updated 16 months ago by 44k • written 19 months ago by • 0
3
votes
3
replies
1.4k
views
how can i filter a sam file from a paf file
paf sam filter
updated 19 months ago by 85k • written 19 months ago by ▴ 10
1
vote
2
replies
1.5k
views
Best way to visualize .paf or .sam alignment to a fasta file
visualization sam fasta paf alignment
updated 19 months ago by 6.8k • written 19 months ago by ▴ 10
0
votes
6
replies
1.1k
views
Mapping paired end reads with ngm and samtools, using prefixes and suffixes for creating vcf eventually
ngm sam samtools
updated 19 months ago by 44k • written 19 months ago by • 0
0
votes
0
replies
453
views
Add HI:i:<n> tag to a BAM file
SAM hisat2 STAR tag BAM
19 months ago by predeus ★ 2.0k
2
votes
2
replies
3.8k
views
BWA alignment score calculation
score SAM BWA alignment
updated 19 months ago by • 0 • written 3.4 years ago by ▴ 20
0
votes
0
replies
493
views
Filtering mapping results by percent identity and aligned percent?
sam bowtie2 minimap2 mapping bwa
20 months ago by kmat • 0
7
votes
3
replies
5.5k
views
how to convert minimap2 generated sam file to bam
minimap2 sam bam samtools
updated 16 months ago by 44k • written 20 months ago by ▴ 50
0
votes
1
reply
458
views
How to count the total read mapped to each chromosome using sam/bam after alignment?
bam sam reads mapped
20 months ago by Diego ▴ 110
8
votes
13
replies
2.1k
views
Mapped reads not mapping to a real sequence?
bam sam samtools kallisto
20 months ago by txema.heredia ▴ 190
2
votes
3
replies
770
views
Mapping with bbmap.sh
bbtools SAM bbmap
updated 21 months ago by 146k • written 21 months ago by ▴ 40
0
votes
6
replies
1.3k
views
STAR is running but .sam file size does not increase after hours mapping
STAR RNA-seq mapping SAM
updated 21 months ago by 146k • written 21 months ago by ▴ 50
50 results • Page 1 of 1
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filterx : fast and efficient filter tool written in Rust for csv,fasta,fastq,gff,vcf,sam files.
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