Question: Unable to convert txt to gtf format
0
gravatar for rajpal22288
3 months ago by
rajpal2228820
Italy
rajpal2228820 wrote:

I am trying to filter some of the noncoding genes from merged.gtf. Although i have extracted them, i am unable to convert them back to gtf format. here's what I am doing:

cat merged.gtf | fgrep -f non-coding-transcript-new.txt > non-coding-transcript.gtf

So basically, i want to match the transcript id's in txt to the id's in merged.gtf and write the final file in gtf format.

And here my non-coding-transcript-new txt file:

transcript_id "#ID transcript_length peptide_length Fickett_score pI ORF_integrity coding_probability label

transcript_id "TCONS_00000022   664     0       0.21719 0.0     -1      0.00838144      noncoding
transcript_id "TCONS_00016027   1639    155     0.31753 6.57525634765625        1       0.739683        coding
transcript_id "TCONS_00016038   2191    106     0.31657 9.64471435546875        1       0.134137        noncoding
transcript_id "TCONS_00016039   2770    106     0.26602000000000003     9.64471435546875        1       0.0926623       noncoding

And merged.gtf:

chr1    chr1    Cufflinks       exon    11869   12227   .       +       .       gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "DDX11L1"; oId "ENST000004563
28.2"; nearest_ref "ENST00000456328.2"; class_code "="; tss_id "TSS1";
chr1    Cufflinks       exon    12613   12721   .       +       .       gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "DDX11L1"; oId "ENST00000456328.2"; n
next-gen python • 152 views
ADD COMMENTlink written 3 months ago by rajpal2228820
0
gravatar for rajpal22288
3 months ago by
rajpal2228820
Italy
rajpal2228820 wrote:

I figured out the problem. the pattern in txt file:

"TCONS_00000022

is not matching up with:

"TCONS_00000003"

in gtf file.

ADD COMMENTlink written 3 months ago by rajpal2228820
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