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<prev • 493 results • page 1 of 17 • next >
1
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1
answer
1.6k
views
1
answer
I can't convert the sam file to fastq file.
fastq sam written 2.6 years ago by porori3000 • 0 • updated 1 day ago by RamRS ♦ 17k
2
votes
1
answer
1.6k
views
1
answer
BLAST geneate Output SAM file , Missing aligned sequences.
blast bam sam output rna-seq written 2.6 years ago by clear.choi • 30 • updated 1 day ago by RamRS ♦ 17k
2
votes
0
answers
634
views
0
answers
softclip vs mismatch at either end
alignment sam written 2.1 years ago by -_- • 650 • updated 6 days ago by Biostar ♦♦ 20
2
votes
2
answers
1.7k
views
2
answers
Problem iterating through BAM file using pysam
python sam bam forloop pysam written 2.6 years ago by c9r1y • 0 • updated 8 days ago by RamRS ♦ 17k
3
votes
1
answer
1.8k
views
1
answer
Extracting Reads by position
alignment sam bam written 2.6 years ago by michael.madans94 • 10 • updated 8 days ago by RamRS ♦ 17k
3
votes
1
answer
177
views
1
answer
Adding optional tags to a BAM file
single-cell bam sam rna-seq awk written 13 days ago by sc243 • 0
0
votes
0
answers
96
views
0
answers
calculating sequencing coverage for metagenome samples
illumina-hi-seq metagenomics sam bowtie2 written 13 days ago by mossigstamboulian • 30
2
votes
1
answer
127
views
1
answer
sam file not showing multi mapped reads
bowtie2 sam written 14 days ago by mossigstamboulian • 30 • updated 13 days ago by RamRS ♦ 17k
9
votes
1
answer
2.3k
views
1
answer
Pysam Parses Certain Read Pairs Out Of Order?
python next-gen samtools sam sequencing written 8.2 years ago by User 9996 • 770 • updated 13 days ago by RamRS ♦ 17k
19
votes
2
answers
6.3k
views
5 follow
2
answers
Going From Cigar String In Sam To Genomic Coordinates?
cigar alignment sam parsing written 8.2 years ago by User 9996 • 770 • updated 13 days ago by RamRS ♦ 17k
9
votes
2
answers
4.9k
views
2
answers
Bwa Sam Output Doubts
alignment format sam output bwa written 8.3 years ago by Seq_Ga • 30 • updated 14 days ago by RamRS ♦ 17k
0
votes
0
answers
120
views
0
answers
Converting .bowtie files to .sam
alignment chip-seq sam bowtie sequencing written 17 days ago by mmitra • 30
4
votes
1
answer
216
views
1
answer
Conversion of sam to bam using samtools
ngs bam samtools sam rna-seq written 7 weeks ago by abhilashreddy495 • 0 • updated 20 days ago by Biostar ♦♦ 20
6
votes
3
answers
188
views
3
answers
How to extract certain tag value by key from sam/bam file?
awk linux samtools sam bash written 22 days ago by yech1990 • 20 • updated 22 days ago by Pierre Lindenbaum ♦ 112k
2
votes
1
answer
131
views
1
answer
SortSam is failing due to Error Parsing SAM file: ("Tag of type i should have signed decimal value")
genome sort sam picard sam written 23 days ago by claudiadast • 0 • updated 23 days ago by Pierre Lindenbaum ♦ 112k
0
votes
1
answer
74
views
1
answer
Solved: BWA ALN cannot not find a very obvious match
alignment sam bwa written 24 days ago by max • 10 • updated 24 days ago by genomax ♦ 55k
2
votes
0
answers
123
views
0
answers
Count exact match reads in SAM file
exactmatch alignment sam written 27 days ago by Agaz Hussain Wani • 40
0
votes
1
answer
128
views
1
answer
Alternative tools for PacBio collapse_isoforms_by_sam.py
sam pacbio collapse written 4 weeks ago by pengchy • 400
1
vote
1
answer
141
views
1
answer
Efficient processing of a read and its mate from bam file
htsjdk java bam samtools sam written 5 weeks ago by mhasa006 • 30 • updated 5 weeks ago by finswimmer ♦ 5.4k
3
votes
2
answers
503
views
2
answers
Iterating through paired-end reads in samtools / pysam
python bam sam written 6 months ago by olavur • 60 • updated 6 weeks ago by gizone1 • 10
2
votes
0
answers
132
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0
answers
Get the regions mapped by the same reads
reads bed bam multiple alignments sam written 6 weeks ago by Corentin • 170
52
votes
1
answer
41k
views
38 follow
1
answer
Number of mapped reads from BAM file
reads bam sam mapping written 3.4 years ago by Prakki Rama • 2.1k • updated 7 weeks ago by iraia.munoa • 10
8
votes
1
answer
2.3k
views
1
answer
Extract Simple Alignment From Sam/Bam
alignment sam written 6.7 years ago by Revh • 60 • updated 7 weeks ago by Biostar ♦♦ 20
4
votes
1
answer
110
views
1
answer
What is chr EBV in human sam file?
bowtie2 sam written 7 weeks ago by salamandra • 170 • updated 7 weeks ago by genomax ♦ 55k
3
votes
1
answer
128
views
1
answer
How do you convert single end sam file to fastq?
samtfastq fastq sam written 7 weeks ago by MAPK • 1.3k • updated 7 weeks ago by Pierre Lindenbaum ♦ 112k
1
vote
1
answer
154
views
1
answer
MACS peak calling of paired-end reads in SAM format
macs chip-seq sam written 7 weeks ago by biostart • 240
7
votes
0
answers
205
views
0
answers
Sort and convert the SAM files to BAM
ngs data analysis samtools rna seq bam sam written 7 weeks ago by amitunited0532 • 0 • updated 7 weeks ago by finswimmer ♦ 5.4k
2
votes
1
answer
142
views
1
answer
Extract the SAM File header section
htsjdk java bam samtools sam written 9 weeks ago by mhasa006 • 30 • updated 9 weeks ago by Pierre Lindenbaum ♦ 112k
6
votes
2
answers
202
views
5 follow
2
answers
Filter sam/bam files
filter bam samtools sam gbs written 3 months ago by ramesh.8v • 200 • updated 3 months ago by swbarnes2 ♦ 4.0k
5
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2
answers
10.0k
views
2
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BWA 0.7.12 and Unique reads, -r, -c options, XA: and SA: optional tags on SAM output,
bwa 0.7.12 unique reads mapping sam written 3.2 years ago by theodore • 40 • updated 3 months ago by Samir • 130
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