producing suited input for IGV by BEDTOOLS toolkit

Question

[jivarajivaraj]

Hello all

I aligned some of read to reference genome by bowtie2 and created sam file, now may someone please describe for me step by step that how I can produce an output that is suited as an input file for the Genome browser or IGV visualising tools using BEDTOOLS toolkit

Thanks

Answer 1

[Giovanni M Dall'Olio]

IGV should be able to read the sam format directly. In alternative you can convert it to bam using:

samtools view -Sb  <myfile.sam>  >  <myfile.bam>

[jivarajivaraj]

Thank you

I already converted sam to bam but my supervisor exactly asked me "select the needed program from the BEDTOOLS toolkit and try to produce an output that is suited as an input file for the Genome browser or IGV visualising tools"

I mean how I can view the generated output by IGV while even I don know how to launch IGV itself?

[Giovanni M Dall'Olio]

I recommend you to read IGV's instructions on the broad website. There are also some excellent video tutorials in youtube on launching and using IGV.

[jivarajivaraj]

Thank you

I'm trying to understand