bioinformatics

Soon after SAM/BAM format became standard for short-read alignment softwares, high caliber tools have been emerging that can process the widely accepted format. bedtools is one of them and it’s easy to use and flexible.

In an earlier [post]({{ ref “post/perl-one-liner-to-process-sequence-files-in-stream.md” }}) we learned how to use Bio::SeqIO module to process fasta files with one-liner. Let’s do more with this capability. What about selecting random sequences from a fasta file?

Circos is a very powerful tool to visualize different types of data (expression, homology, etc) in circular fashion. The software is capable of producing very large images if desired, suitable for posters.

Need a practical way to process fasta files with Bio::SeqIO module ? Below code will print sequence id and sequence length with tab per line. perl -MBio::SeqIO -e '$seq=Bio::SeqIO->new(-fh=>\text{*}STDIN);while($myseq=$seq->next_seq){print $myseq->id,"\text{t}",$myseq->length,"\n";}' < filename OR