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process_minimap2_alignments.pl Script Does Not Accept --incl_out_gff3 Parameter #5
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Hi,
This should work. Which version of Trinity are you using?
…On Sun, Jan 28, 2024 at 2:37 AM Xiaowen ***@***.***> wrote:
image.png (view on web)
<https://github.com/NCIP/Trinity_CTAT/assets/88259108/35386f86-5c8c-4b48-9a2d-a7fc9de1a1f4>
Hello,
I've been working with the process_minimap2_alignments.pl script and
encountered an issue where the script does not seem to accept the
--incl_out_gff3 parameter. When I attempt to use this parameter, it does
not produce the expected output (i.e., the
trinity_GG/Trinity-GG.fasta.mm2.bam.gff3 file), and this is causing errors
in the subsequent steps of my processing pipeline.
Could you please confirm if the --incl_out_gff3 parameter is supported by
this script? If it is supported, I may need guidance on how to properly use
it. Otherwise, is there an alternative approach or workaround that you
could suggest?
Thank you for your time and assistance in resolving this issue.
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--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
|
Also, can you provide the full command you're running?
…On Sun, Jan 28, 2024 at 1:41 PM Brian Haas ***@***.***> wrote:
Hi,
This should work. Which version of Trinity are you using?
On Sun, Jan 28, 2024 at 2:37 AM Xiaowen ***@***.***> wrote:
> image.png (view on web)
> <https://github.com/NCIP/Trinity_CTAT/assets/88259108/35386f86-5c8c-4b48-9a2d-a7fc9de1a1f4>
> Hello,
>
> I've been working with the process_minimap2_alignments.pl script and
> encountered an issue where the script does not seem to accept the
> --incl_out_gff3 parameter. When I attempt to use this parameter, it does
> not produce the expected output (i.e., the
> trinity_GG/Trinity-GG.fasta.mm2.bam.gff3 file), and this is causing errors
> in the subsequent steps of my processing pipeline.
>
> Could you please confirm if the --incl_out_gff3 parameter is supported by
> this script? If it is supported, I may need guidance on how to properly use
> it. Otherwise, is there an alternative approach or workaround that you
> could suggest?
>
> Thank you for your time and assistance in resolving this issue.
>
> —
> Reply to this email directly, view it on GitHub
> <#5>, or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ABZRKX5XBB6UZ2CDFRAXK2DYQX55DAVCNFSM6AAAAABCN7DTCGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYDIMBRGY3TENQ>
> .
> You are receiving this because you are subscribed to this thread.Message
> ID: ***@***.***>
>
--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
|
Certainly, here is the output when I enter the command: Trinity version: Trinity-v2.13.2 |
The full command is |
Hi,
Can you use our singularity image for running STAR-Fusion? It should
have Trinity and everything else needed:
https://github.com/STAR-Fusion/STAR-Fusion/wiki#want-to-use-singularity
best,
Brian
…On Mon, Jan 29, 2024 at 6:52 AM Xiaowen ***@***.***> wrote:
Also, can you provide the full command you're running?
… <#m_5785766631960571089_>
On Sun, Jan 28, 2024 at 1:41 PM Brian Haas *@*.*> wrote: Hi, This should
work. Which version of Trinity are you using? On Sun, Jan 28, 2024 at
2:37 AM Xiaowen @.*> wrote: > image.png (view on web) >
https://github.com/NCIP/Trinity_CTAT/assets/88259108/35386f86-5c8c-4b48-9a2d-a7fc9de1a1f4
> Hello, > > I've been working with the process_minimap2_alignments.pl
script and > encountered an issue where the script does not seem to accept
the > --incl_out_gff3 parameter. When I attempt to use this parameter, it
does > not produce the expected output (i.e., the >
trinity_GG/Trinity-GG.fasta.mm2.bam.gff3 file), and this is causing errors
> in the subsequent steps of my processing pipeline. > > Could you please
confirm if the --incl_out_gff3 parameter is supported by > this script? If
it is supported, I may need guidance on how to properly use > it.
Otherwise, is there an alternative approach or workaround that you > could
suggest? > > Thank you for your time and assistance in resolving this
issue. > > — > Reply to this email directly, view it on GitHub > <#5
<#5>>, or unsubscribe >
https://github.com/notifications/unsubscribe-auth/ABZRKX5XBB6UZ2CDFRAXK2DYQX55DAVCNFSM6AAAAABCN7DTCGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYDIMBRGY3TENQ
> . > You are receiving this because you are subscribed to this
thread.Message > ID: *@*.***> > -- -- Brian J. Haas The Broad Institute
http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas
http://broad.mit.edu/~bhaas
The full command is
STAR-Fusion --CPU 20
--genome_lib_dir ${LIB} -J Chimeric.out.junction --left_fq fastp.R1.gz
--right_fq fastp.R2.gz --output_dir star-fusion
--FusionInspector validate --denovo_reconstruct --examine_coding_effect
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
|
Hello,
I've been working with the process_minimap2_alignments.pl script and encountered an issue where the script does not seem to accept the --incl_out_gff3 parameter. When I attempt to use this parameter, it does not produce the expected output (i.e., the trinity_GG/Trinity-GG.fasta.mm2.bam.gff3 file), and this is causing errors in the subsequent steps of my processing pipeline.
Could you please confirm if the --incl_out_gff3 parameter is supported by this script? If it is supported, I may need guidance on how to properly use it. Otherwise, is there an alternative approach or workaround that you could suggest?
Thank you for your time and assistance in resolving this issue.
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