Comments (7)
zhpn1024
commented on July 19, 2024
It seems that the transcript exon position is not correct.
At 2024-01-22 08:49:54, "haowBio" ***@***.***> wrote:
ribotish predict -b ${bams} -g ${gtf} -f ${fa} -o ${res_dir}/longest_pred.txt -p 40 --longest -v -v after run this code, I got the following error
image.png (view on web)
How can I deal with it?
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haowBio
commented on July 19, 2024
It seems that the transcript exon position is not correct. At 2024-01-22 08:49:54, "haowBio" @.> wrote: ribotish predict -b ${bams} -g ${gtf} -f ${fa} -o ${res_dir}/longest_pred.txt -p 40 --longest -v -v after run this code, I got the following error image.png (view on web) How can I deal with it? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response. How can I find out which transcript is causing the problem, or how can I check the GTF file to identify such errors?
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zhpn1024
commented on July 19, 2024
You can rerun use -p 1 (default) to process genes sequentially, and use -v -v to show processed genes. The error gene would be the next after the log reported gene in the gtf file.
At 2024-01-24 09:58:36, "haowBio" ***@***.***> wrote:
It seems that the transcript exon position is not correct. At 2024-01-22 08:49:54, "haowBio" @.> wrote: ribotish predict -b ${bams} -g ${gtf} -f ${fa} -o ${res_dir}/longest_pred.txt -p 40 --longest -v -v after run this code, I got the following error image.png (view on web) How can I deal with it? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response. How can I find out which transcript is causing the problem, or how can I check the GTF file to identify such errors?
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haowBio
commented on July 19, 2024
You can rerun use -p 1 (default) to process genes sequentially, and use -v -v to show processed genes. The error gene would be the next after the log reported gene in the gtf file. At 2024-01-24 09:58:36, "haowBio" @.> wrote: It seems that the transcript exon position is not correct. At 2024-01-22 08:49:54, "haowBio" @.> wrote: ribotish predict -b ${bams} -g ${gtf} -f ${fa} -o ${res_dir}/longest_pred.txt -p 40 --longest -v -v after run this code, I got the following error image.png (view on web) How can I deal with it? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.> Thank you for your response. How can I find out which transcript is causing the problem, or how can I check the GTF file to identify such errors? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.>
Resolved, but I have another question. If I have multiple samples, how should I use the 'predict' function? Should I run it separately for each sample's BAM file and then merge the ORF results, or should I add all the BAM files after the -b parameter?
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zhpn1024
commented on July 19, 2024
I think if you want just all ORFs in these samples, you can run one predict function with all bam files parameter like `-b sample1.bam,sample2.bam,sample3.bam`. If you want to compare the translation difference between samples, you can run separately.
At 2024-01-24 17:38:40, "haowBio" ***@***.***> wrote:
You can rerun use -p 1 (default) to process genes sequentially, and use -v -v to show processed genes. The error gene would be the next after the log reported gene in the gtf file. At 2024-01-24 09:58:36, "haowBio" @.> wrote: It seems that the transcript exon position is not correct. At 2024-01-22 08:49:54, "haowBio" @.> wrote: ribotish predict -b ${bams} -g ${gtf} -f ${fa} -o ${res_dir}/longest_pred.txt -p 40 --longest -v -v after run this code, I got the following error image.png (view on web) How can I deal with it? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.> Thank you for your response. How can I find out which transcript is causing the problem, or how can I check the GTF file to identify such errors? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.>
Resolved, but I have another question. If I have multiple samples, how should I use the 'predict' function? Should I run it separately for each sample's BAM file and then merge the ORF results, or should I add all the BAM files after the -b parameter?
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haowBio
commented on July 19, 2024
compare the translation difference between samples
Is translation difference referring to calculating through DESeq2 by utilizing the ORF inframecount computed from each sample?
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zhpn1024
commented on July 19, 2024
Yes. Also any other differences you may want to compare.
At 2024-01-25 16:39:06, "haowBio" ***@***.***> wrote:
compare the translation difference between samples
Is translation difference referring to calculating through DESeq2 by utilizing the ORF inframecount computed from each sample?
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