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How to extract required lines of particular chromosome from a gtf file?

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?

rna-seq gtf linux command
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updated by Ram Ram • written by Biologist Biologist

1 answer

You can grep for chr3 (or any such identifier) or use awk to match the query identifier to just the first column, then pipe that output to split -l 1000 to split the output every 1000 lines. I'd recommend using the -d flag in split to get numeric suffixes.

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written by Ram Ram

I actually didd grep like this grep -w chr3 sample.annotated.gtf > chr3.gtf. Could you please show me an example command

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written by Biologist Biologist

Try running split -d -l 10 chr3.gtf chr3_chunks.. Then, with the help of the manual (man split), customize it to your liking.

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written by Ram Ram

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