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2
votes
0
answers
104
views
0
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samtools sort stuck during merging
next-gen samtools bamtools sort written 15 days ago by Carlo Yague • 3.0k
9
votes
1
answer
230
views
1
answer
samtools sorting and indexing
index samtools sort written 27 days ago by ggman • 40 • updated 27 days ago by John ♦ 11k
1
vote
0
answers
131
views
0
answers
sorting bowtie2 results using samtools sort
bowtie2 samtools sort written 29 days ago by ggman • 40
32
votes
8
answers
18k
views
10 follow
8
answers
Efficient And Fastest Way To Sort Large (>100Gb) Bam Files?
picard samtools bam sort written 5.4 years ago by Rm ♦ 7.5k • updated 5 weeks ago by cmdcolin • 640
6
votes
1
answer
112
views
1
answer
Samtools sorting by read names vs. chromosomal coordinates
alignment samtools sort written 6 weeks ago by ropolocan • 270
3
votes
3
answers
483
views
5 follow
3
answers
Trouble with bedtools groupby - not summarizing by columns
bedtools groupby bam sort written 7 months ago by yarmda • 0 • updated 11 weeks ago by Eichan • 10
72
votes
5
answers
36k
views
19 follow
5
answers
Is My Bam File Sorted ?
sequencing next-gen bam sort written 6.5 years ago by Pierre Lindenbaum ♦ 96k • updated 3 months ago by martin.triska • 40
17
votes
6
answers
4.7k
views
8 follow
6
answers
Remove duplicates in fasta file based on ID
fasta sed sort written 2.2 years ago by oliver.bayfield • 90 • updated 5 months ago by Eslam Samir • 90
1
vote
1
answer
331
views
1
answer
Is there a way to tell PLINK and VCFtools to sort the samples in a particular order?
bed vcftools plink ped sort written 6 months ago by beausoleilmo • 80 • updated 6 months ago by chrchang523 • 2.4k
0
votes
0
answers
286
views
0
answers
Allele frequencies sorted IGV visualisation
allele frequency igv af sort written 7 months ago by Palani Kannan • 30
5
votes
0
answers
522
views
0
answers
Sort fastq file by coordinate
fastq alignment bam sort written 9 months ago by Beñat • 20 • updated 7 months ago by Biostar ♦♦ 20
9
votes
4
answers
559
views
4
answers
Script to sort bam file not working
bam samtools unix blast sort written 8 months ago by emth4657 • 10 • updated 8 months ago by Santosh Anand • 2.7k
3
votes
2
answers
521
views
2
answers
Custom sam sort
bam sam rna-seq sort written 11 months ago by thomas.smith2 • 70
0
votes
1
answer
359
views
1
answer
a problem when ran vcf-sort
vcf dict sort written 11 months ago by zengtony743 • 60
2
votes
1
answer
403
views
1
answer
Samtools Sort Error
bam samtools sort written 12 months ago by Valeria • 10
7
votes
1
answer
453
views
1
answer
How to sort chromosome name in bed file
bedfile chrmosome sort written 12 months ago by raya.girish • 20 • updated 12 months ago by genomax ♦ 31k
16
votes
1
answer
788
views
1
answer
Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
bedtools bed sort uniq bash written 13 months ago by QVINTVS_FABIVS_MAXIMVS • 1.9k • updated 13 months ago by ATPoint • 580
6
votes
0
answers
1.2k
views
0
answers
Tutorial: bedGraphToBigWig Tutorial and Report
expecting tutorial bedgraphtobigwig error sort written 17 months ago by Shicheng Guo • 4.4k
16
votes
3
answers
4.9k
views
6 follow
3
answers
Is the Picard SortSam queryname or coordinate equivalent to samtools sort -n?
picard samtools sort written 3.1 years ago by jon.brate • 130 • updated 16 months ago by John ♦ 11k
3
votes
1
answer
742
views
1
answer
Sorted vs unsorted SAM/BAM
bam samtools sam sort written 16 months ago by ofonov • 10 • updated 16 months ago by mastal511 • 1.7k
1
vote
0
answers
563
views
0
answers
How to sort fastq.gz files efficiently
fastq.gz sort written 16 months ago by komal.rathi • 2.9k
5
votes
2
answers
1.5k
views
2
answers
RNA-Seq Analysis: To sort or not to Sort?
htseq myposts sam rna-seq sort written 20 months ago by kanika.151 • 50 • updated 20 months ago by h.mon ♦ 7.5k
3
votes
1
answer
595
views
1
answer
Joining two files with multiple columns
perl grep awk join sort written 21 months ago by vharshavardhanan • 30 • updated 21 months ago by michael.ante • 1.6k
6
votes
4
answers
925
views
4
answers
How to know if samtools sort exited normally [left temporary files behind]
chip-seq ngs next-gen samtools sort written 22 months ago by Sukhdeep Singh ♦ 8.9k • updated 22 months ago by Carlo Yague • 3.0k
9
votes
2
answers
1.4k
views
2
answers
coverage bed error but produces output file
bedtools ngs sort written 22 months ago by cmccabe • 100 • updated 22 months ago by James Ashmore • 1.7k
6
votes
0
answers
1.0k
views
0
answers
Tool: Sorting bed files with bash sort
bash tool bed file sort written 24 months ago by QVINTVS_FABIVS_MAXIMVS • 1.9k
7
votes
1
answer
1.4k
views
1
answer
Size of BAM file reduces after sorting with samtools
genome sequence next-gen samtools sort written 2.0 years ago by shakeelbiochemist • 0 • updated 2.0 years ago by Sean Davis ♦ 23k
1
vote
1
answer
986
views
1
answer
samtools sort remapped bam by readname/query name
bam samtools sort written 2.1 years ago by quachtina96 • 20 • updated 2.1 years ago by Pierre Lindenbaum ♦ 96k
15
votes
4
answers
1.8k
views
14 follow
4
answers
sam/bam file handling -> new tools?
bam sort markduplicates sam written 2.4 years ago by Richard • 490 • updated 2.4 years ago by lh3 ♦ 30k
9
votes
1
answer
3.3k
views
5 follow
1
answer
Mark Duplicates from Picard does not seem to recognize my sorted BAM files.
picard samtools markduplicates bam sort written 3.3 years ago by Jordan • 1.0k • updated 2.7 years ago by 1013002214 • 0
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