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0
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1
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103
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1
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Inside a .sam file, how do I know which read maps where to which scaffold in the assembly?
fasta assembly sam written 3 days ago by fullmooninu • 0 • updated 3 days ago by colindaven • 2.4k
4
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0
answers
144
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5 follow
0
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Revert bam to fastq
bam sam written 26 days ago by MAPK • 1.6k • updated 26 days ago by h.mon ♦ 31k
3
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0
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153
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0
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Tool: SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
viewer read sam tool written 27 days ago by Juke34 • 4.8k
3
votes
1
answer
200
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1
answer
Finding a gene signature among multiple group
rnaseq signature sam written 5 weeks ago by Rahil • 170 • updated 5 weeks ago by Kevin Blighe ♦ 66k
3
votes
1
answer
1.8k
views
1
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Hg19 Strand Information Of Sam Output.
illumina paired-end sam hg19 written 6.6 years ago by Coryza • 30 • updated 6 weeks ago by Biostar ♦♦ 20
1
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1
answer
185
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1
answer
Extract base information from aligned reads in a sam file
reads basepair sam written 10 weeks ago by yliueagle • 220
38
votes
5
answers
553
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12 follow
5
answers
Forum: Why does bioinformatics use a special format like a BAM file instead of a database like SQLite?
forum bam samtools sam written 10 weeks ago by 2xijok • 50 • updated 9 weeks ago by Jeremy Leipzig ♦ 19k
4
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1
answer
237
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5 follow
1
answer
Paired-End Reads and Variant Calling
fastq sam bwa written 12 weeks ago by ocortes • 0 • updated 12 weeks ago by h.mon ♦ 31k
2
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1
answer
1.4k
views
1
answer
Error running sam-dump
ncbi bam samtools sam written 4.0 years ago by beausoleilmo • 330 • updated 12 weeks ago by Biostar ♦♦ 20
0
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1
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189
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1
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Wiggle Files, BAM/SAM Help
wiggle bam sam written 3 months ago by dylan.t.fossl • 0 • updated 3 months ago by jkkbuddika • 160
0
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0
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137
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0
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How to find all positions of one particular contig to which the short reads have been mapped?
mapping bwa shortreads longreads sam written 3 months ago by Ashi • 10
45
votes
6
answers
43k
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16 follow
6
answers
BAM/SAM to FASTA conversion
bam sam written 5.7 years ago by biolab • 1.2k • updated 3 months ago by kristina.mahan • 100
0
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2
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2.0k
views
2
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Filtering reads aligned to specific chromosome
bamtofastq bedtools bam sam snp written 4.6 years ago by signauncreal • 0 • updated 3 months ago by Biostar ♦♦ 20
31
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6
answers
35k
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19 follow
6
answers
How To Sort Sam File
samtools sam written 6.7 years ago by Chen • 1.0k • updated 3 months ago by Biostar ♦♦ 20
0
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0
answers
174
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0
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bowtie2 '-a' does not return all alignments
bowtie2 alignment sam score written 3 months ago by shim • 10
0
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0
answers
139
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0
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Remove reads where quality score length does not equal sequence length
alignment trimming sequence sam quality score written 3 months ago by elisobel • 0
0
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2
answers
185
views
5 follow
2
answers
How to remove reads with only Ns from bam/sam/cram file?
samtools bam cram sam remove reads written 4 months ago by erik.stricker • 0 • updated 4 months ago by Anand Rao • 320
1
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1
answer
176
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1
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count reads (.sam) mapped to scaffolds with non-standard headers
samtools bbmap sam counts written 4 months ago by rakshy • 0
0
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0
answers
1.3k
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0
answers
Samview from bam file aligned to cDNA reference
bam sam rna-seq written 4.5 years ago by bharata1803 • 470 • updated 4 months ago by Biostar ♦♦ 20
2
votes
2
answers
645
views
2
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Making BAM or SAM files equivalent
alignment popoolation2 sam popoolation bam written 23 months ago by keturner123 • 0 • updated 4 months ago by Biostar ♦♦ 20
0
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2
answers
197
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2
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Filter bam files based on length of contig
assembly metagenomics bam map sam written 5 months ago by susheelbhanu • 0 • updated 5 months ago by ATpoint ♦ 40k
7
votes
2
answers
371
views
2
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quality check of bam files
gatk quality bam sam written 5 months ago by gabri.mochales • 30 • updated 5 months ago by Pierre Lindenbaum ♦ 131k
10
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2
answers
8.4k
views
2
answers
Could Any One Explain What Information Inside Sam File?
sam written 6.6 years ago by M K • 510 • updated 6 months ago by Biostar ♦♦ 20
7
votes
1
answer
279
views
1
answer
Does my .sam file look ok? How to convert it?
sam rna-seq written 6 months ago by tanya_fiskur • 40
0
votes
0
answers
246
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5 follow
0
answers
Keep the paired reads whose length less than 400,000 bp
filter alignment sam rna-seq bam written 6 months ago by ek699 • 0
0
votes
1
answer
220
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1
answer
How convert a fastQ file to a Sam/Bam file
bam sam snp convert written 8 months ago by Adriel Rosa • 0 • updated 7 months ago by Biostar ♦♦ 20
4
votes
3
answers
4.1k
views
5 follow
3
answers
Iterating through paired-end reads in samtools / pysam
python bam sam written 2.6 years ago by olavur • 100 • updated 7 months ago by u3005579 • 0
0
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0
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340
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0
answers
Bedtools intersect vcf and bed files
bedtools bcftools sam written 8 months ago by User000 • 400
0
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0
answers
180
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0
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Parsing SAM output and comparison to IGV
sam rna-seq written 9 months ago by cf556 • 10
1
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0
answers
436
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0
answers
Calculate coverage from SAM file
no header samtools sam coverage written 9 months ago by Nandini • 880 • updated 9 months ago by onestop_data • 260
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