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producing suited input for IGV by BEDTOOLS toolkit

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

next-gen
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updated by Ram Ram • written by jivarajivaraj • jivarajivaraj

1 answer

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>
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updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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?

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updated by Ram Ram • written by jivarajivaraj • jivarajivaraj

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