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Hi Guys,

I have RNA-seq data and want Choose one or more tags to match

thanks

rna-seq genome next-gen
• 1,885 views • link
written by ashkan ashkan

In what way is HTSeq involved in preparing your files?

• 1 views • link
written by Devon Ryan Devon Ryan

I made wig files like this:

import HTSeq
alignment_file = HTSeq.SAM_Reader("accepted_hits.sam")
fragmentsize = 20
coverage = HTSeq.GenomicArray("auto", stranded = True, typecode = 'i')

for alignment in alignment_file:
  if alignment.aligned:
    alignment.iv.length = fragmentsize
    coverage[ alignment.iv] += 1

coverage.write_bedgraph_file ( "plus.wig", "+")
coverage.write_bedgraph_file ( "minus.wig", "-")
• 1 views • link
updated by Devon Ryan Devon Ryan • written by ashkan ashkan

Make your life easier and just use bamCoverage from deepTools.

• 1 views • link
written by Devon Ryan Devon Ryan

thank you so much ryan

• 1 views • link
written by ashkan ashkan

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