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0
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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 9 days ago by dongchenchen • 0 • updated 9 days ago by h.mon ♦ 24k
1
vote
1
answer
143
views
1
answer
Interpro results analysis
column sort written 8 weeks ago by ksenia.jravel • 0
3
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0
answers
250
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0
answers
CD-HIT results without sorting by length
length cd-hit clustering sort written 3 months ago by Anand Rao • 210
20
votes
1
answer
984
views
5 follow
1
answer
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 5 months ago by Charlotte.Herzeel • 130
26
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7
answers
9.7k
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10 follow
7
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Remove duplicates in fasta file based on ID
fasta sed sort written 3.9 years ago by oliver.bayfield • 110 • updated 5 months ago by michau • 10
4
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1
answer
290
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1
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samtools sort: legacy usage
genome metagenomics samtools sort written 5 months ago by c.e.chong • 10 • updated 5 months ago by h.mon ♦ 24k
3
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1
answer
303
views
1
answer
Significant Difference of the File Size between csorted and nsorted BAM file
compress nsort samtools sort csort sort written 8 months ago by Shicheng Guo • 7.4k • updated 5 months ago by Biostar ♦♦ 20
5
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1
answer
268
views
1
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should FASTA files be sorted before indexed with SAMtools?
fasta sort samtools index written 6 months ago by Timze W • 20 • updated 6 months ago by finswimmer ♦ 11k
1
vote
2
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1.3k
views
2
answers
Calculating Average Amino Acid Identity (AAI) using CompareM
sort ani checkm comparem aai written 13 months ago by charles.bridges • 70
3
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1
answer
382
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1
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sorting a BAM file
bam sort written 9 months ago by Bogdan • 720 • updated 9 months ago by Philipp Bayer ♦ 6.0k
2
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0
answers
309
views
0
answers
sort the homo sapiens genes by chromosome with Unix command lines
gene sort written 10 months ago by Huichen03 • 10
1
vote
1
answer
392
views
1
answer
Issue while sorting a file
inconsistency trouble sort written 10 months ago by ricfoz • 20 • updated 10 months ago by drkennetz • 360
4
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1
answer
4.0k
views
1
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Sorting with vcftools for tabix gone wrong
vcf tabix sort vcftools index written 4.6 years ago by axelwilhelm • 100 • updated 11 months ago by Biostar ♦♦ 20
3
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1
answer
869
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1
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Samtools sort error with a bam file
bam samtools rna-seq sort written 12 months ago by Vasu • 320 • updated 12 months ago by Devon Ryan ♦ 89k
2
votes
1
answer
590
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1
answer
How to sort an interleaved fastq file by the barcode (BX:Z:) from the header
barcode header interleaved fastq sort written 13 months ago by guillepalou4 • 0 • updated 13 months ago by Pierre Lindenbaum ♦ 118k
6
votes
1
answer
650
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1
answer
Sorting my .bam with samtools produces differences in the fastq files generated afterwards
fastq next-gen samtools bam sort written 13 months ago by guillepalou4 • 0 • updated 13 months ago by Devon Ryan ♦ 89k
2
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0
answers
435
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0
answers
Sorting file by column, with missing values
sort glimmer awk written 14 months ago by oars • 150
2
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1
answer
1.4k
views
1
answer
How to specify the sort based on name in samtools sort?
htseq bam samtools rna-seq sort written 16 months ago by anc.informatics • 0 • updated 16 months ago by finswimmer ♦ 11k
4
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1
answer
2.7k
views
1
answer
Samtools view command, Exec format error while trying to view a human chromosome region
exec format error region view samtools sort written 17 months ago by ricfoz • 20 • updated 17 months ago by Hussain Ather • 910
4
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3
answers
746
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5 follow
3
answers
unique list based on multiple column
awk sort written 17 months ago by Sam • 100 • updated 17 months ago by aka001 • 190
4
votes
1
answer
990
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1
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featuresCount order sam file?
gtf featurescount rna-seq sort written 20 months ago by noeD • 70 • updated 20 months ago by h.mon ♦ 24k
2
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0
answers
1.1k
views
0
answers
samtools sort stuck during merging
next-gen samtools bamtools sort written 21 months ago by Carlo Yague • 4.4k
25
votes
1
answer
32k
views
8 follow
1
answer
samtools sorting and indexing
index samtools sort written 21 months ago by ggman • 70 • updated 21 months ago by John ♦ 12k
1
vote
0
answers
764
views
0
answers
sorting bowtie2 results using samtools sort
bowtie2 samtools sort written 21 months ago by ggman • 70
36
votes
8
answers
23k
views
11 follow
8
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Efficient And Fastest Way To Sort Large (>100Gb) Bam Files?
picard samtools bam sort written 7.1 years ago by Rm ♦ 7.8k • updated 22 months ago by cmdcolin • 1.2k
8
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1
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1.0k
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1
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Samtools sorting by read names vs. chromosomal coordinates
alignment samtools sort written 22 months ago by ropolocan • 510
3
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3
answers
1.5k
views
5 follow
3
answers
Trouble with bedtools groupby - not summarizing by columns
bedtools groupby bam sort written 2.3 years ago by yarmda • 0 • updated 23 months ago by Eichan • 10
92
votes
5
answers
45k
views
27 follow
5
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Is My Bam File Sorted ?
sequencing next-gen bam sort written 8.2 years ago by Pierre Lindenbaum ♦ 118k • updated 2.0 years ago by martin.triska • 110
1
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1
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1.1k
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1
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Is there a way to tell PLINK and VCFtools to sort the samples in a particular order?
bed vcftools plink ped sort written 2.2 years ago by beausoleilmo • 230 • updated 2.2 years ago by chrchang523 ♦ 4.9k
0
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0
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758
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0
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Allele frequencies sorted IGV visualisation
allele frequency igv af sort written 2.3 years ago by Palani Kannan • 60
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