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14
votes
1
answer
5.7k
views
8 follow
1
answer
Deciphering Cigar
cigar next-gen samtools sam alignment written 7.1 years ago by Leszek ♦ 4.0k • updated 8 days ago by Biostar ♦♦ 20
8
votes
0
answers
199
views
5 follow
0
answers
Pipe SamToFastq, BWA mem not working
gatk sam bwa pipe written 4 weeks ago by abbysue • 10 • updated 21 days ago by Biostar ♦♦ 20
0
votes
0
answers
64
views
0
answers
GATK RevertSamSpark No Max_Discard_Fraction option
gatk sam written 4 weeks ago by aalith • 0
2
votes
2
answers
147
views
2
answers
Having trouble with samtools cat
bam samtools sam written 8 weeks ago by matthew.dambrosio.1 • 0 • updated 7 weeks ago by John Marshall ♦ 1.7k
8
votes
4
answers
9.4k
views
9 follow
4
answers
How To Count The Reads Mapped To Exon And Exon-Exon Junctions?
reads gff exon sam bam written 6.2 years ago by lwc628 • 200 • updated 8 weeks ago by m13113153781 • 0
3
votes
1
answer
110
views
1
answer
bwa job - error with file size
fastq alignment bwa rna-seq sam written 8 weeks ago by Laura SMC • 0
1
vote
1
answer
117
views
1
answer
What are the best tools for analyzing and identifying somatic mutations?
vcf bam snp rna-seq sam written 9 weeks ago by gprashant17 • 60 • updated 9 weeks ago by ATpoint ♦ 21k
0
votes
0
answers
133
views
0
answers
Help in interpreting result of magic-blast on nt database
nt alignment paired-reads sam magic-blast written 9 weeks ago by Fabio Marroni • 2.3k
5
votes
1
answer
188
views
1
answer
What is the accurate order of preprocessing steps in DNA Microarray gene expression analysis?
preprocessing limma sam microarray written 10 weeks ago by J. Smith • 0 • updated 10 weeks ago by Santosh Anand ♦ 4.9k
21
votes
2
answers
1.2k
views
5 follow
2
answers
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 9 months ago by Charlotte.Herzeel • 140
2
votes
0
answers
201
views
0
answers
Best SAM flags to evaluate host contamination
ngs sam written 12 weeks ago by ctseto • 70 • updated 12 weeks ago by finswimmer ♦ 12k
1
vote
0
answers
104
views
0
answers
How can bam file only retain potential variants?
samtools sam bwa written 3 months ago by gerrybio2010 • 0
4
votes
2
answers
843
views
2
answers
CIGAR operations performed according to strand or to read?
sequencing read format sam cigar written 20 months ago by Macspider • 2.8k • updated 3 months ago by shouldsee.gem • 0
0
votes
0
answers
165
views
0
answers
View MAF file and the reference sequence in a genome viewer/annotator along with SAM/BAM?
maf viewer bam sam written 3 months ago by DanielC • 90
1
vote
0
answers
160
views
0
answers
How to split both bam files and annotation files as per chromosome number?
annotation bam sam chr split written 3 months ago by Glory Basumata • 140
1
vote
2
answers
281
views
5 follow
2
answers
do paired end reads both mapped to the same gene appear consecutive to each other in SAM file (using bowtie2)
bowtie2 sam shortreads written 4 months ago by Moses • 70 • updated 4 months ago by Devon Ryan ♦ 91k
5
votes
1
answer
274
views
1
answer
Checking MAPQ=255 (unique mapping) interpretation
mapping sam written 4 months ago by BioinformaticsLad • 130 • updated 4 months ago by Devon Ryan ♦ 91k
3
votes
1
answer
303
views
1
answer
Bam file MC tag as integer
mc bam validatesamfile sam written 4 months ago by chariko • 30
3
votes
2
answers
300
views
2
answers
How to find a variant in a particular position in a bam file only using samtools
bam samtools sam written 4 months ago by tw617 • 30 • updated 4 months ago by swbarnes2 ♦ 6.1k
3
votes
0
answers
456
views
5 follow
0
answers
How to calculate percent identity from sam file?
assembly sam samtools mapping cigar written 5 months ago by O.rka • 110
0
votes
0
answers
171
views
0
answers
Read counts at specific locations in SAM files
sam rna-seq hisat2 written 5 months ago by fogarty.mc • 0
3
votes
2
answers
329
views
2
answers
Finding the number of aligned nucleotides per read in a sam file
cigar stings sam written 10 months ago by ioannis • 30 • updated 5 months ago by jilguero888 • 10
1
vote
1
answer
239
views
1
answer
Subsampling aligned SAM/BAM files for RNA-seq analysis
downsampling bam sam rna-seq subsampling written 5 months ago by mohammedtoufiq91 • 40 • updated 5 months ago by WouterDeCoster ♦ 40k
6
votes
5
answers
4.7k
views
7 follow
5
answers
Collect Read Pairs Where At Least One Read Is Mapped
paired-end samtools sam written 6.2 years ago by fridhackery • 140 • updated 6 months ago by ying.kev • 0
1
vote
0
answers
253
views
0
answers
Sub-sampling RNA-seq data
fastq bam sam rna-seq downsampling written 6 months ago by mohammedtoufiq91 • 40
0
votes
0
answers
290
views
0
answers
Extract reads based on pair orientation
paired end read pair sam bam orientation written 6 months ago by Emilie • 0
8
votes
1
answer
4.3k
views
1
answer
How To Force 'Bwa Samse' To Output Multiple Hits In .Sam Format?
sam bwa written 7.2 years ago by Leonor Palmeira ♦ 3.7k • updated 6 months ago by Biostar ♦♦ 20
7
votes
1
answer
815
views
1
answer
Is there a way to do read filtering (MAPQ> certain value) on a BAM instead of SAM file?
quality bam sam filtering mapq written 8 months ago by msimmer92 • 200
8
votes
3
answers
344
views
6 follow
3
answers
Find bams with identical names and merge them
shell picard samtools sam bam written 7 months ago by brendes • 20 • updated 7 months ago by cpad0112 ♦ 11k
7
votes
1
answer
318
views
1
answer
Best way of Merging Multiple Lanes generated by HiSeq 2000, index BAM or VCF?
wgs sam mapping illumina hiseq written 7 months ago by venuraherath • 20
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