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3 hours ago by

I have gtf file that starts like below:

GL000008.2      StringTie       transcript      19957   20594   .       +       .       transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; xloc "XLOC_000001"; class_code "u"; tss_id "TSS1";
GL000008.2      StringTie       exon    19957   20594   .       +       .       transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "1";
GL000008.2      StringTie       transcript      29530   29803   .       +       .       transcript_id "MSTRG.1.1"; gene_id "MSTRG.1"; xloc "XLOC_000002"; class_code "u"; tss_id "TSS2";
GL000008.2      StringTie       exon    29530   29803   .       +       .       transcript_id "MSTRG.1.1"; gene_id "MSTRG.1"; exon_number "1";
GL000008.2      StringTie       transcript      83390   131159  .       +       .       transcript_id "MSTRG.39.2"; gene_id "MSTRG.39"; xloc "XLOC_000003"; class_code "u"; tss_id "TSS3";
GL000008.2      StringTie       exon    83390   83545   .       +       .       transcript_id "MSTRG.39.2"; gene_id "MSTRG.39"; exon_number "1";
GL000008.2      StringTie       exon    85567   85625   .       +       .       transcript_id "MSTRG.39.2"; gene_id "MSTRG.39"; exon_number "2";
GL000008.2      StringTie       exon    88636   88695   .       +       .       transcript_id "MSTRG.39.2"; gene_id "MSTRG.39"; exon_number "3";
GL000008.2      StringTie       exon    129985  131159  .       +       .       transcript_id "MSTRG.39.2"; gene_id "MSTRG.39"; exon_number "4";
GL000008.2      StringTie       transcript      83390   133972  .       +       .       transcript_id "MSTRG.39.1"; gene_id "MSTRG.39"; xloc "XLOC_000003"; class_code "u"; tss_id "TSS3";
GL000008.2      StringTie       exon    83390   83545   .       +       .       transcript_id "MSTRG.39.1"; gene_id "MSTRG.39"; exon_number "1";
GL000008.2      StringTie       exon    85567   85625   .       +       .       transcript_id "MSTRG.39.1"; gene_id "MSTRG.39"; exon_number "2";
GL000008.2      StringTie       exon    129985  130583  .       +       .       transcript_id "MSTRG.39.1"; gene_id "MSTRG.39"; exon_number "3";
GL000008.2      StringTie       exon    133918  133972  .       +       .       transcript_id "MSTRG.39.1"; gene_id "MSTRG.39"; exon_number "4";

I want to extract line 1-1000, 1001-2000, 2001-3000 from chromosome 3 (chr3) into separate gtf files. How to do that on command line?

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modified 2 hours ago

by

RamRS30k

written
3 hours ago
by

Biologist190



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