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• • Rahul Nayak@rahul

  

  Linux Sort Commands for Bioinformatics

  Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so...

  Tags: Bioinformatics, Computational Biology, Linux, Sort, Example

  3619 days ago

• • Rahul Nayak@rahul

  

  Sort FASTA sequence by length: cat f1.fasta| awk '{if($0 ~ /^>/){printf "%st", $0}else{print length($0)"t"$0}}'| sort -k2n,2| awk '{print $1"n"$3}' > sequence.fasta #Sort #Fasta #Trick #Onliner

  Tags: Sort, Fasta, Trick, Onliner

  3180 days ago

• • Jit@jit.aber

  

  Check if BAM file is sorted or not use: for F in `find . -name "*.bam"`; do echo $F; samtools index ${F} ; done #Sort #BAM #Trick

  Tags: Sort, BAM, Trick

  2861 days ago

• • Jit@jit.aber

  

  Sort and get the best first of duplicated lines $ sort -k3rn file | sort -u -k1,1 #Sort #Duplicated #Value

  Tags: Sort, Duplicated, Value

  1376 days ago

• • Hardeep Kaur@hardeep

  

  sort -k2 -n genome.fa #Sort #Column2 #Bash

  Tags: Sort, Column2, Bash

  2108 days ago

• • Jit@jit.aber

  

  sort the string which combined with string + numeric using bash script. $ sort -V #Sort #sort #number #string

  Tags: Sort, sort, number, string

  1191 days ago

• • Jit@jit.aber

  

  Sort a file with column 2: sort -g -k 2,2 allPacbio.fa.fai > sorted.fai #sort #file #column

  Tags: sort, file, column

  2361 days ago

• • LEGE@lege

  

  How to resolve samtools index error "Chromosome blocks not continuous" ?

  samtools index mappedPairs.sorted.bam return the following error ... [bam_sort_core] merging from 0 files and 2 in-memory blocks...[E::hts_idx_push] Chromosome blocks not continuoussamtools index: failed to create index for "mappedPairs.sorted.bam"

  Tags: samtools, index, sort, bam, reads

  989 days ago