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splicebox / PsiCLASS

Simultaneous multi-sample transcript assembler for RNA-seq data
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Transcripts running in different directions having same gene name #4

Open sagnikbanerjee15 opened 4 years ago

sagnikbanerjee15 commented 4 years ago

Hello,

I was going through the output of PsiCLASS and I noticed that there were 2 overlapping genes on opposite strands that had the same gene id. Could you please look into it?

Thank you.

mourisl commented 4 years ago

Thank you for the information. I'll go back to my gtf files to check whether I had this issue.

mourisl commented 4 years ago

I found this problem in my files as well. I will fix this. Thank you for letting me know!!

mourisl commented 4 years ago

I just updated the code. Could you please give it a try? Thanks.

sagnikbanerjee15 commented 4 years ago

Hello,

I tried out the new updated code. While I could not find the problem you stated, I saw a different kind of issue. Non-overlapping transcripts placed near each other on the same chromosome are assigned to the same gene. Please find attached the image. Is that intentional or is that a bug? image

Thank you.

sagnikbanerjee15 commented 4 years ago

I also noticed that for some adjacent gene models, the gene number varies more than one or sometimes even 2. Please check the example. I guess PsiCLASS generates a gene model but then decides to drop it since it fails to cross some threshold. I was wondering if there is a way to make all the adjacent gene models differ by 1.

image

Thank you.

mourisl commented 4 years ago

For both cases, there could be other samples having them somehow connected together, or have that missing gene id. It's very tricky, I'll see what I can do about this.

sagnikbanerjee15 commented 4 years ago

Hello,

I am experiencing the same problem again. I have used the most updated version of the software. The transcripts 1.342.0 is a uniexon transcript. But there is another transcript with the same name.

Thanks. Screen Shot 2020-02-13 at 4 34 48 PM

sagnikbanerjee15 commented 4 years ago

As I was persuing more, I found that there is one transcript of a gene that was annotated in the opposite direction as compared with its sibling transcripts. Please check 1.342.5

1 PsiCLASS transcript 868881 869552 1000 - . gene_id "1.342"; transcript_id "1.342.1"; FPKM "25.959768"; TPM "84.692629"; cov "276.553400"; sample_cnt "32"; 1 PsiCLASS exon 868881 869370 1000 - . gene_id "1.342"; transcript_id "1.342.1"; exon_number "1"; FPKM "25.959768"; TPM "84.692629"; cov "276.553400"; sample_cnt "32"; 1 PsiCLASS exon 869454 869552 1000 - . gene_id "1.342"; transcript_id "1.342.1"; exon_number "2"; FPKM "25.959768"; TPM "84.692629"; cov "276.553400"; sample_cnt "32"; 1 PsiCLASS transcript 870496 871277 1000 - . gene_id "1.342"; transcript_id "1.342.2"; FPKM "18.810759"; TPM "67.751416"; cov "477.495323"; sample_cnt "4"; 1 PsiCLASS exon 870496 870571 1000 - . gene_id "1.342"; transcript_id "1.342.2"; exon_number "1"; FPKM "18.810759"; TPM "67.751416"; cov "477.495323"; sample_cnt "4"; 1 PsiCLASS exon 870651 871277 1000 - . gene_id "1.342"; transcript_id "1.342.2"; exon_number "2"; FPKM "18.810759"; TPM "67.751416"; cov "477.495323"; sample_cnt "4"; 1 PsiCLASS transcript 877854 880054 1000 - . gene_id "1.342"; transcript_id "1.342.4"; FPKM "0.777561"; TPM "2.638833"; cov "9.731431"; sample_cnt "5"; 1 PsiCLASS exon 877854 878655 1000 - . gene_id "1.342"; transcript_id "1.342.4"; exon_number "1"; FPKM "0.777561"; TPM "2.638833"; cov "9.731431"; sample_cnt "5"; 1 PsiCLASS exon 878735 878810 1000 - . gene_id "1.342"; transcript_id "1.342.4"; exon_number "2"; FPKM "0.777561"; TPM "2.638833"; cov "9.731431"; sample_cnt "5"; 1 PsiCLASS exon 878911 880054 1000 - . gene_id "1.342"; transcript_id "1.342.4"; exon_number "3"; FPKM "0.777561"; TPM "2.638833"; cov "9.731431"; sample_cnt "5"; 1 PsiCLASS transcript 886554 887137 1000 + . gene_id "1.342"; transcript_id "1.342.5"; FPKM "0.974386"; TPM "3.221226"; cov "13.106205"; sample_cnt "7"; 1 PsiCLASS exon 886554 886608 1000 + . gene_id "1.342"; transcript_id "1.342.5"; exon_number "1"; FPKM "0.974386"; TPM "3.221226"; cov "13.106205"; sample_cnt "7"; 1 PsiCLASS exon 886703 886863 1000 + . gene_id "1.342"; transcript_id "1.342.5"; exon_number "2"; FPKM "0.974386"; TPM "3.221226"; cov "13.106205"; sample_cnt "7"; 1 PsiCLASS exon 886992 887137 1000 + . gene_id "1.342"; transcript_id "1.342.5"; exon_number "3"; FPKM "0.974386"; TPM "3.221226"; cov "13.106205"; sample_cnt "7"; 1 PsiCLASS transcript 877854 880054 1000 - . gene_id "1.342"; transcript_id "1.342.6"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS exon 877854 878456 1000 - . gene_id "1.342"; transcript_id "1.342.6"; exon_number "1"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS exon 878540 878655 1000 - . gene_id "1.342"; transcript_id "1.342.6"; exon_number "2"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS exon 878735 878810 1000 - . gene_id "1.342"; transcript_id "1.342.6"; exon_number "3"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS exon 878911 880054 1000 - . gene_id "1.342"; transcript_id "1.342.6"; exon_number "4"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS transcript 868881 871277 1000 - . gene_id "1.342"; transcript_id "1.342.7"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 868881 869370 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "1"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 869454 869552 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "2"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 869658 869782 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "3"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 869875 869962 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "4"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 870144 870227 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "5"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 870313 870407 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "6"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 870496 870571 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "7"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 870651 871277 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "8"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS transcript 883638 890027 1000 - . gene_id "1.342"; transcript_id "1.342.8"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 883638 885937 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "1"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886035 886100 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "2"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886196 886244 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "3"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886393 886460 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "4"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886554 886599 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "5"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886696 886789 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "6"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886878 886940 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "7"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887015 887137 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "8"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887225 887258 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "9"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887368 887430 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "10"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887531 887635 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "11"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887725 889524 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "12"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 889769 890027 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "13"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS transcript 877854 890027 1000 - . gene_id "1.342"; transcript_id "1.342.9"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 877854 878655 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "1"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 878735 878810 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "2"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 878911 879710 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "3"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886235 886244 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "4"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886393 886460 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "5"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886554 886599 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "6"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886696 886789 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "7"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886878 886940 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "8"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887015 887137 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "9"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887225 887258 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "10"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887368 887430 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "11"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887531 887635 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "12"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887725 889524 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "13"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 889769 890027 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "14"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44";1 PsiCLASS transcript 868881 869552 1000 - . gene_id "1.342"; transcript_id "1.342.1"; FPKM "25.959768"; TPM "84.692629"; cov "276.553400"; sample_cnt "32"; 1 PsiCLASS exon 868881 869370 1000 - . gene_id "1.342"; transcript_id "1.342.1"; exon_number "1"; FPKM "25.959768"; TPM "84.692629"; cov "276.553400"; sample_cnt "32"; 1 PsiCLASS exon 869454 869552 1000 - . gene_id "1.342"; transcript_id "1.342.1"; exon_number "2"; FPKM "25.959768"; TPM "84.692629"; cov "276.553400"; sample_cnt "32"; 1 PsiCLASS transcript 870496 871277 1000 - . gene_id "1.342"; transcript_id "1.342.2"; FPKM "18.810759"; TPM "67.751416"; cov "477.495323"; sample_cnt "4"; 1 PsiCLASS exon 870496 870571 1000 - . gene_id "1.342"; transcript_id "1.342.2"; exon_number "1"; FPKM "18.810759"; TPM "67.751416"; cov "477.495323"; sample_cnt "4"; 1 PsiCLASS exon 870651 871277 1000 - . gene_id "1.342"; transcript_id "1.342.2"; exon_number "2"; FPKM "18.810759"; TPM "67.751416"; cov "477.495323"; sample_cnt "4"; 1 PsiCLASS transcript 877854 880054 1000 - . gene_id "1.342"; transcript_id "1.342.4"; FPKM "0.777561"; TPM "2.638833"; cov "9.731431"; sample_cnt "5"; 1 PsiCLASS exon 877854 878655 1000 - . gene_id "1.342"; transcript_id "1.342.4"; exon_number "1"; FPKM "0.777561"; TPM "2.638833"; cov "9.731431"; sample_cnt "5"; 1 PsiCLASS exon 878735 878810 1000 - . gene_id "1.342"; transcript_id "1.342.4"; exon_number "2"; FPKM "0.777561"; TPM "2.638833"; cov "9.731431"; sample_cnt "5"; 1 PsiCLASS exon 878911 880054 1000 - . gene_id "1.342"; transcript_id "1.342.4"; exon_number "3"; FPKM "0.777561"; TPM "2.638833"; cov "9.731431"; sample_cnt "5"; 1 PsiCLASS transcript 886554 887137 1000 + . gene_id "1.342"; transcript_id "1.342.5"; FPKM "0.974386"; TPM "3.221226"; cov "13.106205"; sample_cnt "7"; 1 PsiCLASS exon 886554 886608 1000 + . gene_id "1.342"; transcript_id "1.342.5"; exon_number "1"; FPKM "0.974386"; TPM "3.221226"; cov "13.106205"; sample_cnt "7"; 1 PsiCLASS exon 886703 886863 1000 + . gene_id "1.342"; transcript_id "1.342.5"; exon_number "2"; FPKM "0.974386"; TPM "3.221226"; cov "13.106205"; sample_cnt "7"; 1 PsiCLASS exon 886992 887137 1000 + . gene_id "1.342"; transcript_id "1.342.5"; exon_number "3"; FPKM "0.974386"; TPM "3.221226"; cov "13.106205"; sample_cnt "7"; 1 PsiCLASS transcript 877854 880054 1000 - . gene_id "1.342"; transcript_id "1.342.6"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS exon 877854 878456 1000 - . gene_id "1.342"; transcript_id "1.342.6"; exon_number "1"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS exon 878540 878655 1000 - . gene_id "1.342"; transcript_id "1.342.6"; exon_number "2"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS exon 878735 878810 1000 - . gene_id "1.342"; transcript_id "1.342.6"; exon_number "3"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS exon 878911 880054 1000 - . gene_id "1.342"; transcript_id "1.342.6"; exon_number "4"; FPKM "3.942552"; TPM "13.482508"; cov "54.178443"; sample_cnt "47"; 1 PsiCLASS transcript 868881 871277 1000 - . gene_id "1.342"; transcript_id "1.342.7"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 868881 869370 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "1"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 869454 869552 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "2"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 869658 869782 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "3"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 869875 869962 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "4"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 870144 870227 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "5"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 870313 870407 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "6"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 870496 870571 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "7"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS exon 870651 871277 1000 - . gene_id "1.342"; transcript_id "1.342.7"; exon_number "8"; FPKM "37.146890"; TPM "125.780618"; cov "498.604749"; sample_cnt "47"; 1 PsiCLASS transcript 883638 890027 1000 - . gene_id "1.342"; transcript_id "1.342.8"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 883638 885937 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "1"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886035 886100 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "2"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886196 886244 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "3"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886393 886460 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "4"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886554 886599 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "5"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886696 886789 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "6"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 886878 886940 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "7"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887015 887137 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "8"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887225 887258 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "9"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887368 887430 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "10"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887531 887635 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "11"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 887725 889524 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "12"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS exon 889769 890027 1000 - . gene_id "1.342"; transcript_id "1.342.8"; exon_number "13"; FPKM "2.728446"; TPM "9.443200"; cov "37.664989"; sample_cnt "47"; 1 PsiCLASS transcript 877854 890027 1000 - . gene_id "1.342"; transcript_id "1.342.9"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 877854 878655 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "1"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 878735 878810 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "2"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 878911 879710 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "3"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886235 886244 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "4"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886393 886460 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "5"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886554 886599 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "6"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886696 886789 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "7"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 886878 886940 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "8"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887015 887137 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "9"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887225 887258 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "10"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887368 887430 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "11"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887531 887635 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "12"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 887725 889524 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "13"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44"; 1 PsiCLASS exon 889769 890027 1000 - . gene_id "1.342"; transcript_id "1.342.9"; exon_number "14"; FPKM "2.113808"; TPM "7.078307"; cov "1.187879"; sample_cnt "44";

mourisl commented 4 years ago

Thanks for the example! I'm looking into this now.

sagnikbanerjee15 commented 4 years ago

Hello,

This is fixed now.

Thanks.