Records for useful commands in bioinformatics analysis

The post collects my daily used commands or scripts in bioinformatics analysis especially focusing on next generation sequencing.

File format transfer

#####Bed to GTF or Gff

I usually use this online tool, bedToGtf.

Still, there are several ways to do this which I have not tested.

• scripture

java -Xmx1000m -jar <path_to_scripture>/scripture_alpha2.jar -task toGFF -cufflinks -in your_file.bed -source SCRIPTURE -out your_file.gtf

• bedToGenePred

bedToGenePred input.bed stdout | genePredToGtf file stdin output.gtf

• one-line script

awk '{print $1"\t"$7"\t"$8"\t"($2+1)"\t"$3"\t"$5"\t"$6"\t"$9"\t"(substr($0, index($0,$10)))}' foo.bed > bed.gtf # one easy command to generate gtf

Gtf to bed

• gtf2bed from bedops

# (< a file) simply means read in the file
$ gtf2bed < foo.gtf | sort-bed - > foo.bed 

• gtf2bed.pl from clipper

 $ perl gtf2bed.pl input.gtf > output.bed 

• If you want to get the 5’UTR, CDS, 3’UTR, start-codon and stop codon separately, I recommend use my own script parseGTF.py and sortGTF.py. Please see detailed usage for this script in parseGTF.

sortGTF.py gtf-file >sorted.gtf-file
parseGTF.py sorted.gtf-file chrom-sizes-file >gtf.bed

• GTF to Bed12 (use UCSC tools)

gtfToGenePred mm9.gtf stdout | genePredToBed stdin mm9.bed12

Sequence extraction

• Extract FATSA sequence for gtf file
  • gffread from cufflinks

gffread -w output.fa -g gename_assembl.fa refgene.gtf

• Extract FATSA sequence for bed file
  • I recmmend my script seqExtract.3.py

seqExtract.3.py -i genome.fa -b "bed1,bed2..."