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<prev • 555 results • page 1 of 19 • next >
31
votes
6
answers
34k
views
19 follow
6
answers
How To Sort Sam File
samtools sam written 6.4 years ago by Chen • 990 • updated 4 hours ago by Biostar ♦♦ 20
0
votes
0
answers
64
views
0
answers
bowtie2 '-a' does not return all alignments
bowtie2 alignment sam score written 3 days ago by shim • 10
0
votes
0
answers
51
views
0
answers
Remove reads where quality score length does not equal sequence length
alignment trimming sequence sam quality score written 2 days ago by elisobel • 0
0
votes
2
answers
118
views
5 follow
2
answers
How to remove reads with only Ns from bam/sam/cram file?
samtools bam cram sam remove reads written 25 days ago by erik.stricker • 0 • updated 25 days ago by Anand Rao • 310
1
vote
1
answer
89
views
1
answer
count reads (.sam) mapped to scaffolds with non-standard headers
samtools bbmap sam counts written 27 days ago by rakshy • 0
0
votes
0
answers
1.3k
views
0
answers
Samview from bam file aligned to cDNA reference
bam sam rna-seq written 4.2 years ago by bharata1803 • 460 • updated 27 days ago by Biostar ♦♦ 20
2
votes
2
answers
575
views
2
answers
Making BAM or SAM files equivalent
alignment popoolation2 sam popoolation bam written 19 months ago by keturner123 • 0 • updated 4 weeks ago by Biostar ♦♦ 20
0
votes
2
answers
107
views
2
answers
Filter bam files based on length of contig
assembly metagenomics bam map sam written 6 weeks ago by susheelbhanu • 0 • updated 6 weeks ago by ATpoint ♦ 36k
7
votes
2
answers
194
views
2
answers
quality check of bam files
gatk quality bam sam written 8 weeks ago by gabri.mochales • 30 • updated 8 weeks ago by Pierre Lindenbaum ♦ 129k
10
votes
2
answers
8.2k
views
2
answers
Could Any One Explain What Information Inside Sam File?
sam written 6.3 years ago by M K • 500 • updated 11 weeks ago by Biostar ♦♦ 20
7
votes
1
answer
229
views
1
answer
Does my .sam file look ok? How to convert it?
sam rna-seq written 3 months ago by tanya_fiskur • 30
0
votes
0
answers
184
views
5 follow
0
answers
Keep the paired reads whose length less than 400,000 bp
filter alignment sam rna-seq bam written 3 months ago by ek699 • 0
0
votes
1
answer
173
views
1
answer
How convert a fastQ file to a Sam/Bam file
bam sam snp convert written 5 months ago by Adriel Rosa • 0 • updated 3 months ago by Biostar ♦♦ 20
4
votes
3
answers
3.6k
views
5 follow
3
answers
Iterating through paired-end reads in samtools / pysam
python bam sam written 2.3 years ago by olavur • 100 • updated 3 months ago by u3005579 • 0
0
votes
0
answers
212
views
0
answers
Bedtools intersect vcf and bed files
bedtools bcftools sam written 4 months ago by User000 • 380
0
votes
0
answers
133
views
0
answers
Parsing SAM output and comparison to IGV
sam rna-seq written 5 months ago by cf556 • 10
1
vote
0
answers
269
views
0
answers
Calculate coverage from SAM file
no header samtools sam coverage written 5 months ago by Nandini • 840 • updated 5 months ago by onestop_data • 260
0
votes
1
answer
246
views
1
answer
understanding pysam.AlignmentFile output
bam pysam sam written 5 months ago by bitpir • 180 • updated 5 months ago by onestop_data • 260
11
votes
2
answers
7.2k
views
2
answers
Issue with naming convention in bedtools
bedtools sam written 5.2 years ago by A. Domingues • 2.2k • updated 6 months ago by Biostar ♦♦ 20
2
votes
2
answers
5.1k
views
6 follow
2
answers
Insert Size For Illumina Gaiix Paired-End Library From Sam/Bam File
illumina next-gen sam bam written 7.9 years ago by bioinfo • 750 • updated 7 months ago by Gabriel R. • 2.7k
1
vote
1
answer
165
views
1
answer
Is there any way to avoid adding the PG tag while creating a SAM output from BWA ?
pg sam bwa written 7 months ago by lakhujanivijay ♦ 5.1k • updated 7 months ago by Devon Ryan ♦ 95k
3
votes
0
answers
210
views
0
answers
Working With Large *.Bam Files
software error bam sam written 7 months ago by cdc421 • 0 • updated 7 months ago by zx8754 ♦ 9.4k
0
votes
0
answers
164
views
0
answers
Alignment Score (AS) tag in minimap2
minimap2 alignment sam written 7 months ago by tim.booth • 20
8
votes
1
answer
804
views
6 follow
1
answer
Pipe SamToFastq, BWA mem not working
gatk sam bwa pipe written 12 months ago by abbysue • 10 • updated 7 months ago by Marco Pessoa • 0
3
votes
2
answers
276
views
2
answers
SAM flags needed for paired-end strand-specific differential expression
alignment samtools sam rna-seq written 8 months ago by Etstevens • 0 • updated 8 months ago by kristoffer.vittingseerup • 3.3k
1
vote
0
answers
462
views
0
answers
Counting abundance of each gene in SAM/BAM file
gene bam samtools sam abundance written 8 months ago by Hansen_869 • 20
1
vote
2
answers
2.7k
views
2
answers
Identifying The Mismatched Bases And Their Locations On The Chromosome In .Sam File
sam written 7.2 years ago by soosus • 80 • updated 8 months ago by Biostar ♦♦ 20
0
votes
1
answer
226
views
1
answer
exon-intron reads in neuron samples
alignment sam rna-seq bam written 8 months ago by rgescudero • 30 • updated 8 months ago by geek_y ♦ 11k
1
vote
1
answer
210
views
1
answer
Reconstruct reference sequence from SAM file?
sam written 8 months ago by eholleman • 0 • updated 8 months ago by WouterDeCoster ♦ 44k
0
votes
1
answer
210
views
1
answer
Counting starting and ending positions of reads in reference genome
bedtools ngs bam sam rna-seq written 9 months ago by bobbyle0210 • 10 • updated 9 months ago by Pierre Lindenbaum ♦ 129k
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