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7.9 years ago

ashkan ▴ 160

Hi Guys,

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

thanks

RNA-Seq genome next-gen • 1.2k views

ADD COMMENT • link 7.8 years ago by ashkan ▴ 160

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In what way is HTSeq involved in preparing your files?

ADD REPLY • link 7.9 years ago by Devon Ryan 104k

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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", "-")

ADD REPLY • link updated 7.9 years ago by Devon Ryan 104k • written 7.9 years ago by ashkan ▴ 160

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Make your life easier and just use bamCoverage from deepTools.

ADD REPLY • link 7.9 years ago by Devon Ryan 104k

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thank you so much ryan

ADD REPLY • link 7.8 years ago by ashkan ▴ 160

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See here.

ADD REPLY • link 7.9 years ago by Devon Ryan 104k

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