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process_minimap2_alignments.pl Script Does Not Accept --incl_out_gff3 Parameter #5

Open luckyvivi opened 7 months ago

luckyvivi commented 7 months ago

image 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.

brianjohnhaas commented 7 months ago

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 https://github.com/NCIP/Trinity_CTAT/issues/5, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5XBB6UZ2CDFRAXK2DYQX55DAVCNFSM6AAAAABCN7DTCGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYDIMBRGY3TENQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

brianjohnhaas commented 7 months ago

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 https://github.com/NCIP/Trinity_CTAT/issues/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

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

luckyvivi commented 7 months ago

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

Certainly, here is the output when I enter the command: Trinity --version

Trinity version: Trinity-v2.13.2

luckyvivi commented 7 months ago

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

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

brianjohnhaas commented 7 months ago

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? … <#m5785766631960571089> 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 https://github.com/NCIP/Trinity_CTAT/issues/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

— Reply to this email directly, view it on GitHub https://github.com/NCIP/Trinity_CTAT/issues/5#issuecomment-1914536318, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZ3M6QXY7QRXXHXSZLYQ6EOJAVCNFSM6AAAAABCN7DTCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJUGUZTMMZRHA . You are receiving this because you commented.Message ID: @.***>

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas