gffread

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*** stack smashing detected ***: gffread terminated

6

Hi, when i ran gffread, there was a bug. How should id resolve it. Thanks. Code and bug info: (m6A) [dengy@mu01 00_genome]$ gffread -T Ath_genomic.gff -o 1235 *** stack smashing...

dengyang111

GffObj::getSpliced() error: improper

2

Hi Gffread gave me this error when I ran gffread /home/longjh/20220414ticds/basicdata/jy.v2.gff3 -g YGL1.fasta -x ygl1.fa FASTA index file YGL1.fasta.fai created. GffObj::getSpliced() error: improper genomic coordinate 57282209 on Chr09 for evm.model.Chr09.1612...

abcdefghijklmn97

Large genome or large chromosome

4

Hi, I found that gffread (v0.12.7.) can not deal with large chromosomes, we may find minus coordinates when using gffread to deal with such large chromosomes, for example, for a...

xiekunwhy

Hi, developer, Please delete this post. I tried to delete my post but there is no such option provided. Thanks,

santataRU

What does the -r option do in gffread?

1

Hi, Can someone explain to me what the -r option does in gffread? I have read that it: "only shows transcripts overlapping coordinate range .. (on chromosome/contig , strand if...

zigge90

-E prints errors but cannot find a way to write errors to a file

1

I ran the following... gffread -E problemGTF.gtf -o test.gtf ....in effort to find 0 exon transcripts. I cannot find any error flags in the test.gtf file, meaning they were only...

Angsty-Wondergirl

gffread to protein

3

Hello, I tried to extract the coding proteins FASTA from gtf file but the output looks like the following; command used: gffread -y output_protein.fasta -g genome.fasta transcripts.gff3 output; LYT.WSHVP.QTLQSHR.CPSRLLELCSSPLLQMTIHGA.YSFGE.HIMYDIKLDNLQYVRSW.LRKLKL LVQLDKFRTCHP.TPC.SS.TSLDRLHQPAHACLWCGQQWWQYRGLVRQSQSSR.QRSYRTQLVGWREQ....

bijendrabio

Hello, I have tried numerous times to get the "-S" option to work. But I never can get the "*" at the end of full-length proteins. Can this be fixed?...

sanyalab

gffread -w works but not -x and -y

2

Hi there, thanks for developing this very useful tool! I tried to use it to extract CDS and protein from a genome and corresponding gff file. It works with `-w`...

Ruiqi-CUB

I had 200 samples to exact genes cds, so I used "gffread -x" to get my fasta documents, but a part of samples had finished this work. the other samples...

710744562