0 of 0 SJ met filtering criteria and retained

[trianaptx]

head(marvel$sj.metadata) coord.intron gene_short_name.start gene_short_name.end sj.type 1 1:10078:10178 start_unknown.gene|end_unknown.gene 2 1:10084:10178 start_unknown.gene|end_unknown.gene 3 1:10090:10178 start_unknown.gene|end_unknown.gene 4 1:10096:10178 start_unknown.gene|end_unknown.gene 5 1:10102:10178 start_unknown.gene|end_unknown.gene 6 1:10896:10969 start_unknown.gene|end_unknown.gene

marvel <- ValidateSJ.10x(MarvelObject=marvel) #同一基因 500462 unannotated SJ identified SJ metadata and SJ count matrix updated head(marvel$sj.metadata) [1] coord.intron gene_short_name.start gene_short_name.end sj.type

<0 rows> (or 0-length row.names)

hello, could you please tell me what wrong with it, is it a problem of gtf file, or their is some thing wrong in the process of STARsolo? I can run this function normaly previous,but these days I came this bug.Thank you very much if you can address this.

[wenweixiong]

I believe the issue is with the GTF file, I may need to update the function to accommodate the newer format of GTF. May you share your R object here or to my work email (sean.wen@astrazeneca.com) after running CreateMarvelObject.10x function please?

[trianaptx]

Sure，but I will use the Gmail，with a link of Google Drive in that email.发自我的手机-------- 原始邮件 --------发件人： Sean Wen @.>日期： 2023年10月26日周四 晚上8:29收件人： wenweixiong/MARVEL @.>抄送： trianaptx @.>, Author @.>主 题： Re: [wenweixiong/MARVEL] 0 of 0 SJ met filtering criteria and retained (Issue #28) I believe the issue is with the GTF file, I may need to update the function to accommodate the newer format of GTF. May you share your R object here or my work email @.***) after running CreateMarvelObject.10x function please?

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

[wenweixiong]

Hi, I have diagnosed the issue and found that the splice junction coordinates are missing the "chr" prefix.

Please may you add "chr" prefix (see featureData.txt file under Splice junction counts section of the tutorial: https://wenweixiong.github.io/MARVEL_Droplet.html).

Alternatively, you may add the "chr" prefix to the row.names of the splice junction count matrix after creating the MARVEL object:

row.names(marvel$sj.count.matrix) <- paste("chr", row.names(marvel$sj.count.matrix), sep="")

I tried the latter and re-run AnnotateGenes.10x(MarvelObject=marvel) and marvel <- AnnotateSJ.10x(MarvelObject=marvel), and now the splice junctions are annotated with the corresponding genes.

[trianaptx]

Thank you very much!!!