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<prev • 502 results • page 1 of 17 • next >
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Filtering SAM file based on column numbers
filter alignment sam written 8 days ago by elena.syp • 0 • updated 8 days ago by Pierre Lindenbaum ♦ 114k
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1
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212
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1
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sam file not showing multi mapped reads
bowtie2 sam written 9 weeks ago by mossigstamboulian • 30 • updated 10 days ago by Biostar ♦♦ 20
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1
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128
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1
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Get genes and coverage/depth per gene from sam/bam
ngs bam sam coverage per gene depth per gene written 14 days ago by prishly • 0 • updated 14 days ago by Charles Warden ♦ 5.6k
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555
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Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
bam sam sort markduplicates bqsr tool written 23 days ago by Charlotte.Herzeel • 110 • updated 22 days ago by Leonor Palmeira ♦ 3.6k
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112
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1
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Why does bowtie2 Terminate with: Saw ASCII character 10 but expected 33-based Phred qual....?
bowtie2 sam mapping signleread written 23 days ago by jaqx008 • 40 • updated 23 days ago by Istvan Albert ♦♦ 78k
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108
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How to ignore truncation error with PySam?
python sam alignment mapping pysam written 29 days ago by O.rka • 60 • updated 25 days ago by Biostar ♦♦ 20
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1
answer
139
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1
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A constant problem with SAM file header
software error bowtie2 sam written 29 days ago by popescuiofelia • 0 • updated 29 days ago by h.mon ♦ 21k
3
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1
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102
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1
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Finding the number of aligned nucleotides per read in a sam file
cigar stings sam written 29 days ago by ioannis • 30 • updated 29 days ago by Pierre Lindenbaum ♦ 114k
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1
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469
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How to extract sequence message from SAM?
bed sam sequencing written 18 months ago by Jeason Rad • 30 • updated 5 weeks ago by Biostar ♦♦ 20
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1
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150
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8 follow
1
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Merge multiple Sam files to one big Sam file. How?
overlapzscore samtools sam heatmap written 6 weeks ago by jaqx008 • 40 • updated 6 weeks ago by gocougs • 0
4
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1
answer
142
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1
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Position of aligned read in SAM file.
sam bwa written 6 weeks ago by relinquisheddragon • 0
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1.6k
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1
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I can't convert the sam file to fastq file.
fastq sam written 2.7 years ago by porori3000 • 0 • updated 7 weeks ago by RamRS ♦ 19k
2
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1
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1.6k
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1
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BLAST geneate Output SAM file , Missing aligned sequences.
blast bam sam output rna-seq written 2.7 years ago by clear.choi • 30 • updated 7 weeks ago by RamRS ♦ 19k
3
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705
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softclip vs mismatch at either end
alignment sam written 2.2 years ago by -_- • 710 • updated 8 weeks ago by Biostar ♦♦ 20
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2
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1.8k
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2
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Problem iterating through BAM file using pysam
python sam bam forloop pysam written 2.7 years ago by c9r1y • 0 • updated 8 weeks ago by RamRS ♦ 19k
3
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1
answer
1.8k
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1
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Extracting Reads by position
alignment sam bam written 2.7 years ago by michael.madans94 • 10 • updated 8 weeks ago by RamRS ♦ 19k
3
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1
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236
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1
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Adding optional tags to a BAM file
single-cell bam sam rna-seq awk written 9 weeks ago by sc243 • 0
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153
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calculating sequencing coverage for metagenome samples
illumina-hi-seq metagenomics sam bowtie2 written 9 weeks ago by mossigstamboulian • 30
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Pysam Parses Certain Read Pairs Out Of Order?
python next-gen samtools sam sequencing written 8.3 years ago by User 9996 • 790 • updated 9 weeks ago by RamRS ♦ 19k
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2
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5 follow
2
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Going From Cigar String In Sam To Genomic Coordinates?
cigar alignment sam parsing written 8.3 years ago by User 9996 • 790 • updated 9 weeks ago by RamRS ♦ 19k
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2
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5.0k
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2
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Bwa Sam Output Doubts
alignment format sam output bwa written 8.4 years ago by Seq_Ga • 30 • updated 9 weeks ago by RamRS ♦ 19k
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183
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Converting .bowtie files to .sam
alignment chip-seq sam bowtie sequencing written 9 weeks ago by mmitra • 30
4
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1
answer
473
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1
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Conversion of sam to bam using samtools
ngs bam samtools sam rna-seq written 3 months ago by abhilashreddy495 • 0 • updated 10 weeks ago by Biostar ♦♦ 20
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3
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294
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3
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How to extract certain tag value by key from sam/bam file?
awk linux samtools sam bash written 10 weeks ago by yech1990 • 20 • updated 10 weeks ago by Pierre Lindenbaum ♦ 114k
2
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1
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174
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1
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SortSam is failing due to Error Parsing SAM file: ("Tag of type i should have signed decimal value")
genome sort sam picard sam written 10 weeks ago by claudiadast • 0 • updated 10 weeks ago by Pierre Lindenbaum ♦ 114k
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118
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1
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Solved: BWA ALN cannot not find a very obvious match
alignment sam bwa written 10 weeks ago by max • 10 • updated 10 weeks ago by genomax ♦ 58k
2
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0
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179
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Count exact match reads in SAM file
exactmatch alignment sam written 11 weeks ago by Agaz Hussain Wani • 40
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1
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209
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1
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Alternative tools for PacBio collapse_isoforms_by_sam.py
sam pacbio collapse written 12 weeks ago by pengchy • 400
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1
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178
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1
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Efficient processing of a read and its mate from bam file
htsjdk java bam samtools sam written 3 months ago by mhasa006 • 30 • updated 3 months ago by finswimmer ♦ 6.8k
4
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2
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747
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2
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Iterating through paired-end reads in samtools / pysam
python bam sam written 7 months ago by olavur • 70 • updated 3 months ago by gizone1 • 20
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