Hello everybody.
I am having troubles using the MISO pipeline for finding alternative first exons on my reads dataset.
for making MISO work, an index must be created by the index_gff.py script which comes with the pipelne. According to the MISO webiste, the input should be like this one:
Instead, a normal GFF file downloaded from ensEMBL looks like this
so the indexer is not recognizing some part, as described by the error log:
[CODEWARNING: Invalid attributes string: gene_id "ENSDARG00000074181"; transcript_id "ENSDART00000057160"; exon_number "1"; gene_name "LRRC24 (2 of 2)"; gene_biotype "protein_coding"; transcript_name "CT027690.1-201";[/CODE]
I would like to change the script (which is in python) but since I don't know the indexing criterias I don't know how to do it. Has some already done this, or know a way to make this script indexing work?
thank you very much,
daniele
I am having troubles using the MISO pipeline for finding alternative first exons on my reads dataset.
for making MISO work, an index must be created by the index_gff.py script which comes with the pipelne. According to the MISO webiste, the input should be like this one:
chr1 SE gene 4772649 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-;Name=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-
chr1 SE mRNA 4772649 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-
chr1 SE mRNA 4772649 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-
chr1 SE exon 4775654 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A.up;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A
chr1 SE exon 4774032 4774186 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A.se;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A
chr1 SE exon 4772649 4772814 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A.dn;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A
chr1 SE exon 4775654 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B.up;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B
chr1 SE exon 4772649 4772814 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B.dn;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B
chr1 SE mRNA 4772649 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-
chr1 SE mRNA 4772649 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-
chr1 SE exon 4775654 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A.up;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A
chr1 SE exon 4774032 4774186 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A.se;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A
chr1 SE exon 4772649 4772814 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A.dn;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.A
chr1 SE exon 4775654 4775821 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B.up;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B
chr1 SE exon 4772649 4772814 . - . ID=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B.dn;Parent=chr1:4775654:4775821:-@chr1:4774032:4774186:-@chr1:4772649:4772814:-.B
11 protein_coding exon 31158398 31158571 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "2"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31158398 31158571 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "2"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31161221 31161385 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "3"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31161221 31161385 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "3"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31161542 31162705 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "4"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31161542 31162705 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "4"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31165694 31165819 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "5"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31165694 31165819 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "5"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31167191 31167313 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "6"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31167191 31167313 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "6"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31167542 31167667 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "7"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31167542 31167667 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "7"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31168516 31168641 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "8"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31168516 31168641 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "8"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31168791 31168945 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "9"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31168791 31168942 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "9"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding stop_codon 31168943 31168945 . + 0 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "9"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31158398 31158571 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "2"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31161221 31161385 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "3"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31161221 31161385 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "3"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31161542 31162705 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "4"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31161542 31162705 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "4"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31165694 31165819 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "5"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31165694 31165819 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "5"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31167191 31167313 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "6"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31167191 31167313 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "6"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31167542 31167667 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "7"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31167542 31167667 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "7"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31168516 31168641 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "8"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31168516 31168641 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "8"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding exon 31168791 31168945 . + . gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "9"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
11 protein_coding CDS 31168791 31168942 . + 2 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "9"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201"; protein_id "ENSDARP00000111013";
11 protein_coding stop_codon 31168943 31168945 . + 0 gene_id "ENSDARG00000091602"; transcript_id "ENSDART00000122756"; exon_number "9"; gene_name "CR790368.1"; gene_biotype "protein_coding"; transcript_name "CR790368.1-201";
[CODEWARNING: Invalid attributes string: gene_id "ENSDARG00000074181"; transcript_id "ENSDART00000057160"; exon_number "1"; gene_name "LRRC24 (2 of 2)"; gene_biotype "protein_coding"; transcript_name "CT027690.1-201";[/CODE]
I would like to change the script (which is in python) but since I don't know the indexing criterias I don't know how to do it. Has some already done this, or know a way to make this script indexing work?
thank you very much,
daniele
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