Vipin
Looking into this.
Just need to clarify one thing - the first file which you mentioned is not a GFF file. To me, the lines look like in GTF form. Primarily this program...
Sorry for the delay, I didn't see much need for a GBK file for handling the feature annotation back in that day and decided to retire the program from the...
Hi @ramadatta, Can I have first few lines from your GFF3 input file?
@ramadatta the input gff3 file lines looks good to me. From the above error message, I am seeing little difference the current version of the code: `https://github.com/vipints/GFFtools-GX/blob/master/gff_to_bed.py#L87`. Can you test...
@ramadatta can you provide me the ncbi link where you downloaded the gff3 file.
Hi @ramadatta, I have downloaded the file from the above link. There are many features available in this GFF file. `cut -f 2,3 ref_ASM185804v2_top_level.gff3 | sort | uniq -c` The...
in BED format we are representing the transcript feature in a single line.
I could do something that I can kick out these non properly matched annotation features. But I m not sure whether this will clean all single exon gene annotation from...
Thanks for the detailed list of many awesome datasets! few missing good data source from biology side: GTEx _http://www.gtexportal.org/_ ESP(Exome Sequencing Project) _https://esp.gs.washington.edu/drupal/_ ExAC(Exome Aggregation Consortium) _http://exac.broadinstitute.org/_ UK10K _http://www.uk10k.org/_