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  • hailongcorn
    Junior Member
    • May 2014
    • 6
    #1

    help:combine interesting gff and tophat bedfile

    I have a problem unsolved,listed below
    I get one gff file which contains interesting genes,transcripts,exon,intron etc.eg:
    9 ensembl gene 19154953 19164082 . + . ID=GRMZM2G443985;Name=GRMZM2G443985;biotype=protein_coding
    9 ensembl mRNA 19154953 19160236 . + . ID=GRMZM2G443985_T01;Parent=GRMZM2G443985;Name=GRMZM2G443985_T01;biotype=protein_coding
    9 ensembl intron 19155466 19156260 . + . Parent=GRMZM2G443985_T01;Name=intron.9805
    9 ensembl intron 19156308 19156394 . + . Parent=GRMZM2G443985_T01;Name=intron.9806
    9 ensembl intron 19156435 19156543 . + . Parent=GRMZM2G443985_T01;Name=intron.9807
    9 ensembl intron 19156607 19156733 . + . Parent=GRMZM2G443985_T01;Name=intron.9808
    9 ensembl intron 19156872 19157016 . + . Parent=GRMZM2G443985_T01;Name=intron.9809
    9 ensembl intron 19157176 19157333 . + . Parent=GRMZM2G443985_T01;Name=intron.9810
    9 ensembl intron 19157388 19157527 . + . Parent=GRMZM2G443985_T01;Name=intron.9811
    9 ensembl intron 19157597 19157714 . + . Parent=GRMZM2G443985_T01;Name=intron.9812
    9 ensembl intron 19157845 19158737 . + . Parent=GRMZM2G443985_T01;Name=intron.9813
    9 ensembl intron 19158779 19158877 . + . Parent=GRMZM2G443985_T01;Name=intron.9814
    9 ensembl intron 19159100 19159294 . + . Parent=GRMZM2G443985_T01;Name=intron.9815
    9 ensembl intron 19159341 19159419 . + . Parent=GRMZM2G443985_T01;Name=intron.9816
    9 ensembl intron 19159575 19159711 . + . Parent=GRMZM2G443985_T01;Name=intron.9817
    9 ensembl exon 19154953 19155465 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E41
    9 ensembl exon 19156261 19156307 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E43
    9 ensembl exon 19156395 19156434 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E10
    9 ensembl exon 19156544 19156606 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E37
    9 ensembl exon 19156734 19156871 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E17
    9 ensembl exon 19157017 19157175 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E07
    9 ensembl exon 19157334 19157387 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E29
    9 ensembl exon 19157528 19157596 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E39
    9 ensembl exon 19157715 19157844 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E11
    9 ensembl exon 19158738 19158778 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E23
    9 ensembl exon 19158878 19159099 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E08
    9 ensembl exon 19159295 19159340 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E19
    9 ensembl exon 19159420 19159574 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E20
    9 ensembl exon 19159712 19160236 . + . Parent=GRMZM2G443985_T01;Name=GRMZM2G443985_E42
    9 ensembl CDS 19155187 19155465 . + . Parent=GRMZM2G443985_T01;Name=CDS.9832
    9 ensembl CDS 19156261 19156307 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9833
    9 ensembl CDS 19156395 19156434 . + 2 Parent=GRMZM2G443985_T01;Name=CDS.9834
    9 ensembl CDS 19156544 19156606 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9835
    9 ensembl CDS 19156734 19156871 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9836
    9 ensembl CDS 19157017 19157175 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9837
    9 ensembl CDS 19157334 19157387 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9838
    9 ensembl CDS 19157528 19157596 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9839
    9 ensembl CDS 19157715 19157844 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9840
    9 ensembl CDS 19158738 19158778 . + 1 Parent=GRMZM2G443985_T01;Name=CDS.9841
    9 ensembl CDS 19158878 19159099 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9842
    9 ensembl CDS 19159295 19159340 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9843
    9 ensembl CDS 19159420 19159574 . + 1 Parent=GRMZM2G443985_T01;Name=CDS.9844
    9 ensembl CDS 19159712 19159885 . + 0 Parent=GRMZM2G443985_T01;Name=CDS.9845
    9 ensembl mRNA 19155187 19164082 . + . ID=GRMZM2G443985_T02;Parent=GRMZM2G443985;Name=GRMZM2G443985_T02;biotype=protein_coding
    9 ensembl intron 19155466 19156260 . + . Parent=GRMZM2G443985_T02;Name=intron.9846
    9 ensembl intron 19156308 19156394 . + . Parent=GRMZM2G443985_T02;Name=intron.9847
    9 ensembl intron 19156435 19156543 . + . Parent=GRMZM2G443985_T02;Name=intron.9848
    9 ensembl intron 19156607 19156733 . + . Parent=GRMZM2G443985_T02;Name=intron.9849
    9 ensembl intron 19156872 19157016 . + . Parent=GRMZM2G443985_T02;Name=intron.9850
    9 ensembl intron 19157176 19157333 . + . Parent=GRMZM2G443985_T02;Name=intron.9851
    9 ensembl intron 19157388 19157527 . + . Parent=GRMZM2G443985_T02;Name=intron.9852
    9 ensembl intron 19157597 19157714 . + . Parent=GRMZM2G443985_T02;Name=intron.9853
    9 ensembl intron 19157845 19158737 . + . Parent=GRMZM2G443985_T02;Name=intron.9854
    9 ensembl intron 19158779 19158877 . + . Parent=GRMZM2G443985_T02;Name=intron.9855
    9 ensembl intron 19159100 19159294 . + . Parent=GRMZM2G443985_T02;Name=intron.9856
    9 ensembl intron 19159341 19159419 . + . Parent=GRMZM2G443985_T02;Name=intron.9857
    9 ensembl intron 19159575 19160730 . + . Parent=GRMZM2G443985_T02;Name=intron.9858
    9 ensembl intron 19161065 19161925 . + . Parent=GRMZM2G443985_T02;Name=intron.9859
    9 ensembl intron 19162122 19162246 . + . Parent=GRMZM2G443985_T02;Name=intron.9860
    9 ensembl intron 19162375 19162557 . + . Parent=GRMZM2G443985_T02;Name=intron.9861
    9 ensembl intron 19162761 19162871 . + . Parent=GRMZM2G443985_T02;Name=intron.9862
    9 ensembl intron 19162998 19163104 . + . Parent=GRMZM2G443985_T02;Name=intron.9863
    9 ensembl intron 19163264 19163338 . + . Parent=GRMZM2G443985_T02;Name=intron.9864
    9 ensembl intron 19163533 19163614 . + . Parent=GRMZM2G443985_T02;Name=intron.9865
    9 ensembl exon 19155187 19155465 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E25
    9 ensembl exon 19156261 19156307 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E34
    9 ensembl exon 19156395 19156434 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E21
    9 ensembl exon 19156544 19156606 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E28
    9 ensembl exon 19156734 19156871 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E04
    9 ensembl exon 19157017 19157175 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E33
    9 ensembl exon 19157334 19157387 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E13
    9 ensembl exon 19157528 19157596 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E18
    9 ensembl exon 19157715 19157844 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E44
    9 ensembl exon 19158738 19158778 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E30
    9 ensembl exon 19158878 19159099 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E32
    9 ensembl exon 19159295 19159340 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E02
    9 ensembl exon 19159420 19159574 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E26
    9 ensembl exon 19160731 19161064 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E24
    9 ensembl exon 19161926 19162121 . + . Parent=GRMZM2G443985_T02;Name=GRMZM2G443985_E14
    Other files I get from tophat are the junction.bed,deletion.bed and insertion.bed,eg:
    chromosome9 19155376 19156307 JUNC00137067 36 + 19155376 19156307 255,0,0 2 89,47 0,884
    chromosome9 19156260 19156434 JUNC00137068 15 + 19156260 19156434 255,0,0 2 47,40 0,134
    chromosome9 19156394 19156606 JUNC00137069 11 + 19156394 19156606 255,0,0 2 40,63 0,149
    chromosome9 19156543 19156794 JUNC00137070 4 + 19156543 19156794 255,0,0 2 63,61 0,190
    chromosome9 19156786 19157101 JUNC00137071 21 + 19156786 19157101 255,0,0 2 85,85 0,230
    chromosome9 19157087 19157387 JUNC00137072 27 + 19157087 19157387 255,0,0 2 88,54 0,246
    chromosome9 19157333 19157596 JUNC00137073 21 + 19157333 19157596 255,0,0 2 54,69 0,194
    chromosome9 19157527 19157802 JUNC00137074 42 + 19157527 19157802 255,0,0 2 69,88 0,187
    chromosome9 19157814 19158174 JUNC00137075 1 + 19157814 19158174 255,0,0 2 30,60 0,300
    chromosome9 19157765 19158826 JUNC00137076 53 + 19157765 19158826 255,0,0 2 79,89 0,972
    chromosome9 19158723 19158964 JUNC00137077 87 + 19158723 19158964 255,0,0 2 55,87 0,154
    chromosome9 19159013 19159340 JUNC00137078 64 + 19159013 19159340 255,0,0 2 86,46 0,281
    chromosome9 19159294 19159508 JUNC00137079 134 + 19159294 19159508 255,0,0 2 46,89 0,125
    chromosome9 19159486 19159789 JUNC00137080 133 + 19159486 19159789 255,0,0 2 88,78 0,225
    chromosome9 19160992 19162008 JUNC00137081 3 + 19160992 19162008 255,0,0 2 72,83 0,933
    chromosome9 19162074 19162331 JUNC00137082 5 + 19162074 19162331 255,0,0 2 47,85 0,172
    chromosome9 19162293 19162638 JUNC00137083 17 + 19162293 19162638 255,0,0 2 81,81 0,264
    chromosome9 19162675 19162960 JUNC00137084 23 + 19162675 19162960 255,0,0 2 85,89 0,196
    chromosome9 19162920 19163191 JUNC00137085 21 + 19162920 19163191 255,0,0 2 77,87 0,184
    chromosome9 19163178 19163427 JUNC00137086 24 + 19163178 19163427 255,0,0 2 85,89 0,160
    chromosome9 19163446 19163679 JUNC00137087 30 + 19163446 19163679 255,0,0 2 86,65 0,168
    the red marked are supporting reads.
    How can i get each gene,exon ,intron and transcript read count from two or more files?Any help?
    Tags: None
    • hailongcorn
      Junior Member
      • May 2014
      • 6
      #2
      anyone help?

        Comment

        • gringer
          David Eccles (gringer)
          • May 2011
          • 845
          #3
          Use cufflinks. That will produce most of the count data that you require (at least gene-level and transcript-level counts). For exon-level, you might need to use DEXSeq -- exon counting is somewhat tricky. I'm not sure about intron counting.

            Comment

            • hailongcorn
              Junior Member
              • May 2014
              • 6
              #4
              thank you.I'll have a try

                Comment

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