Open haowBio opened 8 months ago
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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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?
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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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?
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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compare the translation difference between samples
Is translation difference
referring to calculating through DESeq2 by utilizing the ORF inframecount computed from each sample?
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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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 How can I deal with it?