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really long introns create a problem with gffread #53
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Hello @jkreplak, Thank you so much for your interest in Thank you. |
Hello,
Could you please repost the question? For some reason, I cannot find it on
Github.
Thank you.
Sagnik Banerjee (Ph.D.)
Iowa State University
Applied Bioinformatics Scientist
Bristol Myers Squibb
*"The moment I have realized God sitting in the temple of every human body,
the moment I stand in reverence before every human being and see God in him
- that moment I am free from bondage, everything that binds vanishes, and I
am free" - Swami Vivekananda*
ᐧ
…On Thu, Mar 24, 2022 at 12:58 PM jkreplak ***@***.***> wrote:
Hi,
I've managed to create with agat my own exon-based transcripts fasta and
comment gffread to force finder to use it. It's finished, so that's a
really good news !
However, I'm surprised by the results. Why does the CDS stop before the
stop codon base and not at the end of it in the gtf ?
Is that a bug on my side ?
If not, the official ontology for CDS in the SO include the stop codon and
it should be added.
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Hello, |
Hello @jkreplak, Thank you for reporting this issue. I will create a program that will you can use to filter out certain genes and transcripts. Could you please post a few examples of the output where stop codons are missing? Since the result is being output in GTF mode, there will not be any STOP codon annotated. But later versions of the software will have the option to request for such annotations as well. Thank you. |
Hi,
My Finder crashed during FindCDS at the codan steps. Codan throw an error about duplicate key :
After checking this error, i found in the gtf file combined_split_transcripts_with_bad_SJ_redundancy_removed.gtf
around 650 transcripts with ultra-long introns :
When I relaunch gffread, i can see that the software is creating at least two fasta entry for this transcript, explaining the duplicate message of codan. After checking the web, it seems that gffread has an intron limit size.
How can I go around that to finish the pipeline ?
Thanks,
Jonathan
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