Exporting four channel signals abi file
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Entering edit mode
5.9 years ago

Hello all , I want to extract the all 4 nucleotide signal values A T G C , I gone through this post and tried whatever maintained there.When i used following commend

abiview -graph data -outseq myseq.fa myseq.ab1

it generating the 4 files but i m not getting the peak values at each position here is the one output file

##
##Title abiview of Seq_D12_RAJASHEKAR_MITO5_F_008
##Graphs 4
##Number 1
##Points 43
##XminA 801.000000 XmaxA 805.000000 YminA 0.000000 YmaxA 2399.000000
##Xmin 0.000000 Xmax 0.000000 Ymin 0.000000 Ymax 0.000000
##ScaleXmin 801.000000 ScaleXmax 805.000000 ScaleYmin 0.000000 ScaleYmax 2399.000000
##Maintitle 
##Subtitle 
##Xtitle 
##Ytitle 
801.090881  22.000000
801.181824  22.000000
801.272705  22.000000
801.363647  23.000000
801.454529  25.000000
801.545471  27.000000
801.636353  28.000000
801.727295  29.000000
801.818176  29.000000
801.909119  29.000000
802.000000  28.000000
802.083313  27.000000
802.166687  26.000000
802.250000  26.000000
802.333313  27.000000
802.416687  27.000000
802.500000  28.000000
802.583313  30.000000
802.666687  31.000000
802.750000  33.000000
802.833313  34.000000
802.916687  35.000000
803.000000  35.000000
803.090881  34.000000
803.181824  32.000000
803.272705  30.000000
803.363647  29.000000
803.454529  29.000000
803.545471  31.000000
803.636353  33.000000
803.727295  36.000000
803.818176  38.000000
803.909119  37.000000
804.000000  35.000000
804.111084  31.000000
804.222229  26.000000
804.333313  22.000000
804.444458  19.000000
804.555542  18.000000
804.666687  19.000000
804.777771  20.000000
804.888916  21.000000
805.000000  20.000000
 ##DataObjects
##Number 0
##GraphObjects
##Number 4
 Textline x1 801.000000 y1 2349.000000 x2 0.000000 y2 0.000000 colour 1 size 1.0 T
 Textline x1 802.000000 y1 2349.000000 x2 0.000000 y2 0.000000 colour 1 size 1.0 T
 Textline x1 803.000000 y1 2349.000000 x2 0.000000 y2 0.000000 colour 1 size 1.0 T
 Textline x1 804.000000 y1 2349.000000 x2 0.000000 y2 0.000000 colour 1 size 1.0 T

but my sequence length is around 800 bp its not showing the values for the 450 bp in the sequence when i use perl

eperl -MBio::Trace::ABIF -MArray::Transpose -e 'BEGIN{$abif=Bio::Trace::ABIF->new($_); $,="\t",$\="\n"}; $abif-            >open_abif(@ARGV) or die "can not open";  print @$_ foreach transpose ([map {[$_,$abif->raw_trace($_)]} qw(A T G C)])' my.ab1 > my_ab1_trace.tab

its giving me around 16000 rows so can any1 please tell me how to extract details of each signal values

P.S Need to be compatible with linux terminal

genome sequencing • 1.1k views
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