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.
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 gtfGtf 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.bed12Sequence extraction
- Extract FATSA sequence for
gtffile- gffread from cufflinks
gffread -w output.fa -g gename_assembl.fa refgene.gtf- Extract FATSA sequence for
bedfile- I recmmend my script seqExtract.3.py
seqExtract.3.py -i genome.fa -b "bed1,bed2..."