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3
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1
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110
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1
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sambamba-sort: Error reading BGZF with BAM file
software error sort sambamba written 5 weeks ago by marongiu.luigi • 520 • updated 5 weeks ago by ATpoint ♦ 36k
4
votes
1
answer
150
views
1
answer
sorting for bedtools genomecov doesn't work properly
bedtools bedpe sort rna-seq bedgraph written 4 months ago by Assa Yeroslaviz • 1.3k • updated 4 months ago by Kevin Blighe ♦ 61k
28
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2
answers
55k
views
11 follow
2
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samtools sorting and indexing
index samtools sort written 3.0 years ago by ggman • 80 • updated 5 months ago by onestop_data • 260
0
votes
0
answers
145
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0
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How to get unique counts saved in a file
linux awk unique counts sort written 7 months ago by kittys • 0 • updated 7 months ago by genomax ♦ 85k
3
votes
2
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343
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2
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Linux sort P-values with scientific notation
pvalue sort scientific notation written 8 months ago by Shicheng Guo • 8.3k • updated 8 months ago by zx8754 ♦ 9.3k
5
votes
1
answer
264
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1
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How to get chrM chr1 ...chr22 chrX chrY order in my bam file
gatk picard snp bam sort written 8 months ago by Ada • 0 • updated 8 months ago by jkbonfield • 380
2
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1
answer
474
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1
answer
bedtools sort -faidx in CWL
bedtools cwl sort written 13 months ago by dami • 10 • updated 8 months ago by kaushik.ghose • 70
1
vote
1
answer
206
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5 follow
1
answer
Pipe pysam.view() output to pysam.sort()
python sam alignment pysam sort written 9 months ago by Macspider • 3.0k • updated 9 months ago by gb • 1.8k
3
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1
answer
241
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1
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How can I get this sorted by ascending order? (when the number and character is together)
sort written 11 months ago by woojoy14 • 0 • updated 11 months ago by Chris Miller ♦ 21k
21
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2
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2.3k
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5 follow
2
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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 20 months ago by Charlotte.Herzeel • 140
4
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0
answers
398
views
6 follow
0
answers
How to sort sam file using shell script?
sam file forum samtools sort written 13 months ago by gerrybio2010 • 0 • updated 13 months ago by Bastien Hervé ♦ 4.6k
0
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1
answer
831
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1
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bowtie2 piped to samtools created many samtools.tmp.bam files, how to get the single .bam file?
bowtie2 alignment samtools sort written 15 months ago by dongchenchen • 10 • updated 15 months ago by h.mon ♦ 30k
1
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1
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354
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1
answer
Interpro results analysis
column sort written 16 months ago by ksenia.jravel • 0
3
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0
answers
675
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0
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CD-HIT results without sorting by length
length cd-hit clustering sort written 18 months ago by Anand Rao • 300
36
votes
8
answers
14k
views
17 follow
8
answers
Remove duplicates in fasta file based on ID
fasta sed sort written 5.1 years ago by oliver.bayfield • 150 • updated 19 months ago by michau • 50
4
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1
answer
739
views
1
answer
samtools sort: legacy usage
genome metagenomics samtools sort written 20 months ago by c.e.chong • 20 • updated 20 months ago by h.mon ♦ 30k
3
votes
1
answer
486
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1
answer
Significant Difference of the File Size between csorted and nsorted BAM file
compress nsort samtools sort csort sort written 22 months ago by Shicheng Guo • 8.3k • updated 20 months ago by Biostar ♦♦ 20
5
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1
answer
1.1k
views
1
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should FASTA files be sorted before indexed with SAMtools?
fasta sort samtools index written 21 months ago by Timze W • 60 • updated 21 months ago by finswimmer ♦ 13k
1
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2
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2.6k
views
2
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Calculating Average Amino Acid Identity (AAI) using CompareM
sort ani checkm comparem aai written 2.3 years ago by charles.bridges • 70
3
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1
answer
823
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1
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sorting a BAM file
bam sort written 23 months ago by Bogdan • 1000 • updated 23 months ago by Philipp Bayer ♦ 6.7k
2
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0
answers
575
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0
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sort the homo sapiens genes by chromosome with Unix command lines
gene sort written 2.1 years ago by Huichen03 • 20
1
vote
1
answer
601
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1
answer
Issue while sorting a file
inconsistency trouble sort written 2.1 years ago by ricfoz • 30 • updated 2.1 years ago by drkennetz • 500
4
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1
answer
5.0k
views
1
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Sorting with vcftools for tabix gone wrong
vcf tabix sort vcftools index written 5.8 years ago by axelwilhelm • 100 • updated 2.2 years ago by Biostar ♦♦ 20
3
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1
answer
1.7k
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1
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Samtools sort error with a bam file
bam samtools rna-seq sort written 2.3 years ago by Vasu • 450 • updated 2.3 years ago by Devon Ryan ♦ 95k
2
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1
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1.1k
views
1
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How to sort an interleaved fastq file by the barcode (BX:Z:) from the header
barcode header interleaved fastq sort written 2.3 years ago by guillepalou4 • 0 • updated 2.3 years ago by Pierre Lindenbaum ♦ 129k
8
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1
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1.2k
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1
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Sorting my .bam with samtools produces differences in the fastq files generated afterwards
fastq next-gen samtools bam sort written 2.3 years ago by guillepalou4 • 0 • updated 2.3 years ago by Devon Ryan ♦ 95k
2
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0
answers
722
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0
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Sorting file by column, with missing values
sort glimmer awk written 2.4 years ago by oars • 160
2
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1
answer
2.8k
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1
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How to specify the sort based on name in samtools sort?
htseq bam samtools rna-seq sort written 2.6 years ago by anc.informatics • 0 • updated 2.6 years ago by finswimmer ♦ 13k
4
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1
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4.7k
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1
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Samtools view command, Exec format error while trying to view a human chromosome region
exec format error region view samtools sort written 2.6 years ago by ricfoz • 30 • updated 2.6 years ago by Hussain Ather • 940
4
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3
answers
1.0k
views
5 follow
3
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unique list based on multiple column
awk sort written 2.7 years ago by Sam • 140 • updated 2.7 years ago by aka001 • 190
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