Ecosyste.ms: Issues

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GitHub / gpertea/gffread issues and pull requests

#50 - Extract cds/protein/exon sequence name show geneid

Issue - State: open - Opened by liu-wq almost 5 years ago - 4 comments
Labels: feature request

#50 - Extract cds/protein/exon sequence name show geneid

Issue - State: open - Opened by liu-wq almost 5 years ago - 4 comments
Labels: feature request

#49 - Release v0.11.7 to CCB software download page

Issue - State: closed - Opened by jma1991 almost 5 years ago - 2 comments

#49 - Release v0.11.7 to CCB software download page

Issue - State: closed - Opened by jma1991 almost 5 years ago - 2 comments

#48 - conversion of gtf to fasta file?

Issue - State: closed - Opened by mathavanpu almost 5 years ago - 3 comments

#48 - conversion of gtf to fasta file?

Issue - State: closed - Opened by mathavanpu almost 5 years ago - 3 comments

#47 - CDS and protein sequences missing first base when exon line not present

Issue - State: open - Opened by monicabritton almost 5 years ago - 1 comment

#47 - CDS and protein sequences missing first base when exon line not present

Issue - State: open - Opened by monicabritton almost 5 years ago - 1 comment

#46 - Cannot extract attributes when specifying the --table parameter

Issue - State: closed - Opened by jma1991 almost 5 years ago - 2 comments

#46 - Cannot extract attributes when specifying the --table parameter

Issue - State: closed - Opened by jma1991 almost 5 years ago - 2 comments

#45 - missing gene id after converting gff to gtf

Issue - State: closed - Opened by ze236789 almost 5 years ago - 2 comments

#45 - missing gene id after converting gff to gtf

Issue - State: closed - Opened by ze236789 almost 5 years ago - 2 comments

#44 - getGenePositions issue

Issue - State: open - Opened by birsandhu almost 5 years ago

#44 - getGenePositions issue

Issue - State: open - Opened by birsandhu almost 5 years ago

#43 - --no-psuedo option does not seem to work

Issue - State: closed - Opened by lparsons about 5 years ago - 2 comments

#43 - --no-psuedo option does not seem to work

Issue - State: closed - Opened by lparsons about 5 years ago - 2 comments

#42 - Gffread to extract transcript sequences from transcript assembly GTF file

Issue - State: open - Opened by Aishah17 about 5 years ago - 2 comments

#42 - Gffread to extract transcript sequences from transcript assembly GTF file

Issue - State: open - Opened by Aishah17 about 5 years ago - 2 comments

#41 - GVF format

Issue - State: open - Opened by rsalz about 5 years ago

#41 - GVF format

Issue - State: open - Opened by rsalz about 5 years ago

#40 - gffread vs cufflinks

Issue - State: closed - Opened by mestia over 5 years ago - 3 comments

#40 - gffread vs cufflinks

Issue - State: closed - Opened by mestia over 5 years ago - 3 comments

#39 - gffread installation issue

Issue - State: open - Opened by jingjin0322 over 5 years ago - 2 comments

#39 - gffread installation issue

Issue - State: open - Opened by jingjin0322 over 5 years ago - 2 comments

#38 - Gffread command not found

Issue - State: open - Opened by nishagove over 5 years ago - 1 comment

#37 - missing gene_id

Issue - State: closed - Opened by olechnwin over 5 years ago - 4 comments

#37 - missing gene_id

Issue - State: closed - Opened by olechnwin over 5 years ago - 4 comments

#36 - Extract sequence features from BGZIPped genome sequences

Issue - State: open - Opened by lucventurini over 5 years ago - 1 comment
Labels: enhancement

#36 - Extract sequence features from BGZIPped genome sequences

Issue - State: open - Opened by lucventurini over 5 years ago - 1 comment
Labels: enhancement

#35 - BUG? single exon transcripts on - strand incorrectly discarded

Issue - State: closed - Opened by dstern over 5 years ago - 2 comments

#35 - BUG? single exon transcripts on - strand incorrectly discarded

Issue - State: closed - Opened by dstern over 5 years ago - 2 comments

#34 - gffread, Error: no genomic sequence provided!

Issue - State: closed - Opened by Quicken-up over 5 years ago - 2 comments

#34 - gffread, Error: no genomic sequence provided!

Issue - State: closed - Opened by Quicken-up over 5 years ago - 2 comments

#33 - GFF to GTF transformation to use then RSEM

Issue - State: open - Opened by EidrianGM over 5 years ago - 1 comment

#33 - GFF to GTF transformation to use then RSEM

Issue - State: open - Opened by EidrianGM over 5 years ago - 1 comment

#32 - release for 0.10.6 on gff utilities website

Issue - State: closed - Opened by arielzn almost 6 years ago - 1 comment

#31 - Error in gffread to extract transcript seqs

Issue - State: closed - Opened by sarahharvey88 almost 6 years ago - 2 comments

#31 - Error in gffread to extract transcript seqs

Issue - State: closed - Opened by sarahharvey88 almost 6 years ago - 2 comments

#30 - merging overlapping/adjacent feature

Issue - State: closed - Opened by StoltzfusJ about 6 years ago - 4 comments

#30 - merging overlapping/adjacent feature

Issue - State: closed - Opened by StoltzfusJ about 6 years ago - 4 comments

#29 - Conversion to GTF does not convert phase to frame

Issue - State: closed - Opened by channsoden over 6 years ago - 4 comments

#29 - Conversion to GTF does not convert phase to frame

Issue - State: closed - Opened by channsoden over 6 years ago - 4 comments

#28 - GFF Error: overlapping duplicate nucleic_acid feature

Issue - State: open - Opened by minor7b5 over 6 years ago

#28 - GFF Error: overlapping duplicate nucleic_acid feature

Issue - State: open - Opened by minor7b5 over 6 years ago

#27 - query about incomplete conversion from GFF3 to GTF

Issue - State: closed - Opened by prasundutta87 over 6 years ago - 7 comments

#27 - query about incomplete conversion from GFF3 to GTF

Issue - State: closed - Opened by prasundutta87 over 6 years ago - 7 comments

#25 - How is mixed-strand trans-splicing handled?

Issue - State: open - Opened by fruce-ki over 6 years ago - 4 comments
Labels: bug

#25 - How is mixed-strand trans-splicing handled?

Issue - State: open - Opened by fruce-ki over 6 years ago - 4 comments
Labels: bug

#24 - Documentation for "linpack" references?

Issue - State: closed - Opened by tseemann over 6 years ago - 2 comments

#24 - Documentation for "linpack" references?

Issue - State: closed - Opened by tseemann over 6 years ago - 2 comments

#23 - Include GClib files in this project?

Issue - State: closed - Opened by tseemann over 6 years ago - 4 comments

#23 - Include GClib files in this project?

Issue - State: closed - Opened by tseemann over 6 years ago - 4 comments

#22 - How to deal with codon phase to extract the good dna sequence?

Issue - State: closed - Opened by StromTroopers over 6 years ago - 4 comments
Labels: invalid

#22 - How to deal with codon phase to extract the good dna sequence?

Issue - State: closed - Opened by StromTroopers over 6 years ago - 4 comments
Labels: invalid

#21 - gffread handle Mitochondrion gff3 has bugs?

Issue - State: closed - Opened by GuoqiLiu over 6 years ago - 6 comments

#21 - gffread handle Mitochondrion gff3 has bugs?

Issue - State: closed - Opened by GuoqiLiu over 6 years ago - 6 comments

#20 - GTF error for GFF3 file

Issue - State: closed - Opened by sejmodha over 6 years ago - 4 comments

#20 - GTF error for GFF3 file

Issue - State: closed - Opened by sejmodha over 6 years ago - 4 comments

#19 - Off-by-one error

Issue - State: closed - Opened by CDieterich almost 7 years ago - 11 comments

#19 - Off-by-one error

Issue - State: closed - Opened by CDieterich almost 7 years ago - 11 comments

#18 - Segmentation fault

Issue - State: closed - Opened by alephreish almost 7 years ago

#17 - Fix Options mismatch #13

Pull Request - State: closed - Opened by alephreish about 7 years ago

#17 - Fix Options mismatch #13

Pull Request - State: closed - Opened by alephreish about 7 years ago

#16 - Fix Options mismatch #13

Pull Request - State: closed - Opened by alephreish about 7 years ago - 1 comment

#15 - Error getting subseq

Issue - State: closed - Opened by alephreish about 7 years ago - 1 comment

#15 - Error getting subseq

Issue - State: closed - Opened by alephreish about 7 years ago - 1 comment

#14 - Stop codons

Issue - State: closed - Opened by alephreish about 7 years ago - 3 comments

#14 - Stop codons

Issue - State: closed - Opened by alephreish about 7 years ago - 3 comments

#13 - Options mismatch

Issue - State: closed - Opened by alephreish about 7 years ago

#13 - Options mismatch

Issue - State: closed - Opened by alephreish about 7 years ago

#12 - field missing when using option -F

Issue - State: open - Opened by lassancejm about 7 years ago

#12 - field missing when using option -F

Issue - State: open - Opened by lassancejm about 7 years ago

#11 - Link to precompiled OSX binary on jhu.edu broken

Issue - State: closed - Opened by cbrueffer about 7 years ago - 2 comments

#11 - Link to precompiled OSX binary on jhu.edu broken

Issue - State: closed - Opened by cbrueffer about 7 years ago - 2 comments

#10 - the result may be wrong

Issue - State: open - Opened by jiangchb over 7 years ago - 1 comment

#10 - the result may be wrong

Issue - State: open - Opened by jiangchb over 7 years ago - 1 comment

#9 - -O should be more permissive, more faithful to the raw GTF/GFF input

Issue - State: open - Opened by bbimber over 7 years ago - 5 comments
Labels: enhancement

#8 - Case insensitive sorting?

Issue - State: open - Opened by bbimber over 7 years ago - 1 comment
Labels: enhancement

#5 - Line-endings from genomic fasta input are doubled or misplaced in cds fasta output

Issue - State: closed - Opened by culpinnis almost 8 years ago - 1 comment

#4 - End coordinates exceed sequence length when extracting transcripts

Issue - State: open - Opened by roberthaney almost 8 years ago - 1 comment

#3 - GFF3 to GTF: How to preserve gene features in GTF output

Issue - State: open - Opened by guillermomarco over 8 years ago - 4 comments

#2 - *** buffer overflow detected ***: gffread terminated

Issue - State: closed - Opened by bananabenana over 8 years ago - 1 comment

#1 - Error parsing fasta index line

Issue - State: closed - Opened by tantrev over 8 years ago - 6 comments
Labels: bug