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<prev • 477 results • page 1 of 16 • next >
2
votes
1
answer
94
views
1
answer
Extract the SAM File header section
htsjdk java bam samtools sam written 5 days ago by mhasa006 • 30 • updated 4 days ago by Pierre Lindenbaum ♦ 110k
5
votes
2
answers
132
views
5 follow
2
answers
Filter sam/bam files
filter bam samtools sam gbs written 26 days ago by ramesh.8v • 200 • updated 26 days ago by swbarnes2 ♦ 3.8k
5
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2
answers
9.4k
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 3.0 years ago by theodore • 40 • updated 4 weeks ago by Samir • 130
1
vote
1
answer
245
views
1
answer
Iterating through paired-end reads in samtools / pysam
python bam sam written 3 months ago by olavur • 60 • updated 4 weeks ago by Michi • 930
20
votes
3
answers
10k
views
8 follow
3
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Fasta File To Sam Conversion
fasta format sam conversion written 7.2 years ago by Rallapalli Sukeerthi Teja • 10 • updated 5 weeks ago by harishchander.a • 0
0
votes
1
answer
129
views
1
answer
extract one-side unmapped reads from sam
tophat bam samtools sam written 5 weeks ago by liorglic • 40 • updated 5 weeks ago by Carlo Yague • 4.1k
15
votes
2
answers
1.1k
views
7 follow
2
answers
A Question On Doing Substitution By Using Bash
unix sam written 6.9 years ago by Yunfei Li • 280 • updated 6 weeks ago by Biostar ♦♦ 20
4
votes
1
answer
137
views
1
answer
Formula for extracting per base read depth/per base genome coverage from a SAM file?
bedtools alignment samtools sam coverage written 7 weeks ago by Diploid Progenitor • 10 • updated 7 weeks ago by Devon Ryan ♦ 81k
4
votes
3
answers
406
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3
answers
Is there an R function that transforms a decimal SAM FLAG into a list of strings?
flag R bam sam alignment format written 10 months ago by cristian • 110 • updated 8 weeks ago by mathieu.lajoie • 10
0
votes
1
answer
1.1k
views
1
answer
Sam file header and truncated file
header samtools sam written 21 months ago by TriS • 3.4k • updated 8 weeks ago by Volkan Sevim • 0
0
votes
2
answers
371
views
2
answers
Samtools stats "inward oriented pairs" - what flags does this correspond to?
alignment sequence samtools sam bam written 7 months ago by roryC • 0 • updated 9 weeks ago by vo2 • 0
0
votes
1
answer
154
views
1
answer
Error of SAMSequenceDictionary
samtools sam igv written 10 weeks ago by niu.shengyong • 30 • updated 10 weeks ago by genomax ♦ 52k
1
vote
0
answers
153
views
0
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How to check if a read in a Bam file is paired or not?
reads paired reads bam sam single paired reads written 10 weeks ago by omariqbal2017 • 0
3
votes
0
answers
155
views
0
answers
SAM CIGAR parsing and position counter in R
cigar parsing sam R written 10 weeks ago by niu.shengyong • 30
0
votes
0
answers
117
views
0
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Extract unique reads from SAM file
unique reads sam rsamtools written 11 weeks ago by niu.shengyong • 30
5
votes
2
answers
172
views
2
answers
How to convert from a cigar string to extended cigar string?
extended cigar cigar c++ sam bam written 11 weeks ago by omariqbal2017 • 0 • updated 11 weeks ago by genomax ♦ 52k
0
votes
1
answer
174
views
1
answer
How to simply extract certain filed from sam file
assembly samtools sam written 12 weeks ago by 934963534 • 10 • updated 12 weeks ago by swbarnes2 ♦ 3.8k
1
vote
1
answer
206
views
1
answer
What is corrupting my SAM files?
sequence samtools sam bam written 3 months ago by arudhir • 10
1
vote
1
answer
293
views
1
answer
iterate over reads in .SAM file with pysam - IndexError: list index out of range
python pysam sam written 3 months ago by Florian BERNARD • 20 • updated 3 months ago by Pierre Lindenbaum ♦ 110k
0
votes
1
answer
302
views
1
answer
bowtie2 alignment has 'Duplicated sequence'
bowtie2 alignment sam bowtie2-build written 3 months ago by rmash • 0
15
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2
answers
396
views
2
answers
converting RSEM bam output into sam files for DEseq?
sam bam deseq rsem rna-seq written 4 months ago by Sepd • 0
2
votes
0
answers
188
views
0
answers
Generation of Consenses Fasta from SAM/BAM
fasta ngs bam misa sam written 4 months ago by mail2steff • 30
5
votes
2
answers
191
views
2
answers
How to check if a read in a SAM file contains substitutions
read bam sam c++ written 4 months ago by omariqbal2017 • 0 • updated 4 months ago by d-cameron • 1.8k
1
vote
1
answer
233
views
1
answer
What's the difference between half mapped reads and single paired reads?
reads single reads bam sam paired reads written 4 months ago by omariqbal2017 • 0 • updated 4 months ago by d-cameron • 1.8k
1
vote
1
answer
766
views
1
answer
converting SAMRecord to JSON or String format
htsjdk json sam samrecord written 24 months ago by dsvispute91 • 0 • updated 4 months ago by Biostar ♦♦ 20
10
votes
1
answer
3.0k
views
1
answer
Two Fastq Files And Alignment With Bwa.
fastq alignment sam bwa written 6.7 years ago by KCC • 3.9k • updated 4 months ago by Biostar ♦♦ 20
8
votes
2
answers
173
views
2
answers
HISAT output SAM file incorrect (only contains 3 columns of data)
files hisat sam written 4 months ago by emcc • 10
26
votes
6
answers
25k
views
18 follow
6
answers
How To Sort Sam File
samtools sam written 4.4 years ago by Chen • 670 • updated 4 months ago by Biostar ♦♦ 20
3
votes
1
answer
214
views
1
answer
alignment score and other values for the whole paired-end alignment (with overlap)
bowtie2 paired-end alignment sam scores written 4 months ago by shim • 10 • updated 4 months ago by Devon Ryan ♦ 81k
2
votes
3
answers
290
views
6 follow
3
answers
Fastq and sam number of reads
ngs fastq sam written 4 months ago by ceboral • 0 • updated 4 months ago by swbarnes2 ♦ 3.8k
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