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<prev • 852 results • page 1 of 29 • next >
6
votes
2
answers
208
views
2
answers
what should a SAM/BAM record contain when there are no quality scores
bam samtools sam written 1 day ago by Ann • 2.1k • updated 10 hours ago by jkbonfield • 20
2
votes
0
answers
128
views
0
answers
convert bam to clustal
R clustal alignment bioconductor bam written 2 days ago by bioinfo8 • 80
3
votes
1
answer
102
views
1
answer
Strip primer sequences from sequencing reads
amplicon-seq dna-seq bam written 4 days ago by kulvait • 200 • updated 4 days ago by Robert Sicko • 480
0
votes
0
answers
106
views
0
answers
input for Connor: FASTQ files from several lanes
fastq bam connor written 9 days ago by lien • 40
7
votes
1
answer
216
views
5 follow
1
answer
how to adjust BAM header after extracting only mapped reads from BAM files
bam samtools written 7 weeks ago by Ric • 130 • updated 21 days ago by glihm • 400
3
votes
1
answer
134
views
1
answer
Parsing BAM to genome feature
annotation bam sam rna-seq written 22 days ago by dzb • 0 • updated 22 days ago by Devon Ryan ♦ 70k
0
votes
0
answers
145
views
0
answers
Inferring the zygosity of large indels (transposon variants) from bam paired-end mapping to reference and bed coordinate files
indel zygosity alignment samtools bam written 29 days ago by rimjhim.roy.ch • 50
2
votes
1
answer
188
views
1
answer
Add tags to BAM/SAM file
sequencing alignment sam bam rna-seq written 22 days ago by dzb • 0 • updated 22 days ago by Matt Shirley ♦ 7.7k
2
votes
3
answers
269
views
9 follow
3
answers
Download SAM/BAM files from SRA takes ages!!!
sra bam written 24 days ago by Alejandro Jimenez Sanchez • 90 • updated 23 days ago by ghostforever.shi • 10
0
votes
1
answer
181
views
1
answer
Missing header sam file
header chip-seq sam bam written 24 days ago by G.Car • 20 • updated 24 days ago by Pierre Lindenbaum ♦ 96k
3
votes
1
answer
136
views
1
answer
Program to calculate and add the NM tag to a bam file
nm bam written 28 days ago by abascalfederico • 960 • updated 28 days ago by trausch • 650
2
votes
0
answers
136
views
0
answers
Filter single exon reads
single exon reads bam written 29 days ago by sloux • 0
11
votes
1
answer
233
views
6 follow
1
answer
Removing PCR duplicates - fastq or BAM?
duplicates fastq alignment bam written 4 weeks ago by rbronste • 140 • updated 29 days ago by Istvan Albert ♦♦ 73k
1
vote
1
answer
153
views
1
answer
Samtools flagstat unpaired reads
bowtie2 bam samtools written 4 weeks ago by rbronste • 140 • updated 4 weeks ago by Pierre Lindenbaum ♦ 96k
7
votes
1
answer
253
views
1
answer
How to merge/combine previously split bam files?
merge bam alignment bam sequencing written 4 weeks ago by ycsm • 10
9
votes
2
answers
226
views
6 follow
2
answers
BAM to CRAM to BAM
bam cram written 5 weeks ago by ElUretsky • 20 • updated 4 weeks ago by James Bonfield • 110
3
votes
1
answer
133
views
1
answer
deepTools draw coverage for specific region
deeptools alignment bam written 4 weeks ago by Medhat • 6.8k • updated 4 weeks ago by Devon Ryan ♦ 70k
1
vote
0
answers
182
views
0
answers
What does 'TLEN' in BAM file mean if mate pairs aligned to different chromosomes?
alignment bam written 4 weeks ago by verne91 • 10
0
votes
0
answers
144
views
0
answers
Galaxy VarScan SNP size and stderr
varscan galaxy variant bam written 5 weeks ago by louis.gil007 • 0
2
votes
1
answer
170
views
5 follow
1
answer
Why some entries from a same pair in the bam file have different TLEN?
genome 10x alignment bam sequencing written 5 weeks ago by verne91 • 10
2
votes
1
answer
200
views
1
answer
IGV error: Error loading SAM header: For sequence 34711, text and binary have different lengths in file.
bam rna-seq igv written 5 weeks ago by EVR • 430 • updated 5 weeks ago by dyollluap • 270
3
votes
1
answer
148
views
1
answer
Is it okay to realign and subsequently process fastq files that were converted from processed BAM files?
fastq alignment recalibration bwa bam written 5 weeks ago by mary.a.wood.91 • 0 • updated 5 weeks ago by Istvan Albert ♦♦ 73k
11
votes
1
answer
840
views
1
answer
In-place writable BAM files
bgzip bam written 17 months ago by John ♦ 11k • updated 5 weeks ago by Biostar ♦♦ 20
12
votes
2
answers
12k
views
2
answers
BAM/SAM to FASTA conversion
bam sam written 2.5 years ago by biolab • 910 • updated 5 weeks ago by Chadi Saad • 30
1
vote
1
answer
131
views
1
answer
Difference between Alignment quality and Mapping quality
sequence next-gen bam written 5 weeks ago by ammarsabir15 • 50 • updated 5 weeks ago by jh.monin • 10
3
votes
1
answer
134
views
1
answer
Rsamtools and BAM file discordance
reads bam samtools rsamtools igv written 6 weeks ago by cristian • 70 • updated 6 weeks ago by Devon Ryan ♦ 70k
7
votes
1
answer
163
views
6 follow
1
answer
Correct way of merging samples for father, mother, child trio variant calling
vcf variant calling bam written 6 weeks ago by eurioste • 20 • updated 6 weeks ago by Pierre Lindenbaum ♦ 96k
49
votes
5
answers
21k
views
31 follow
5
answers
How to plot coverage and depth statistics of a bam file
sequencing next-gen coverage bam depth written 3.2 years ago by krithika.gu • 150 • updated 7 weeks ago by bioinfo8 • 80
188
votes
11
answers
104k
views
89 follow
11
answers
Tools To Calculate Average Coverage For A Bam File?
bam coverage sequencing written 6.6 years ago by Biomed ♦ 4.2k • updated 7 weeks ago by bioinfo8 • 80
4
votes
1
answer
205
views
1
answer
Extract parts of reads from BAM file that overlap a specific region of genome
alignment bam sequencing written 7 weeks ago by Chadi Saad • 30 • updated 7 weeks ago by Pierre Lindenbaum ♦ 96k
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