Question about the 6th column of spaln gff3 output

[b524198065]

Dear developers,

I got the results from spaln aligning CDS to the reference genome and I want to perform some filters based on the 6th column of the gff3 output (below). Do you have any idea of the cut-off of the 6th scores? Is it proper that any category that under a cut-off (e.g., 300) was eliminated? Thanks.

##sequence-region chr4 244737 263168 chr4 ALN gene 259152 259304 306 + . ID=gene00002;Name=chr4_259 chr4 ALN mRNA 259152 259304 306 + . ID=mRNA00002;Parent=gene00002;Name=chr4_259 chr4 ALN exon 259152 259304 306 + . ID=exon00003;Parent=mRNA00002;Name=chr4_259;Target=43312_Csa64_4G019080.1.fna 1 153 +

[ogotoh]

The sixth column of the gff3 format shows the ‘exon score’, which is calculated from sequence alignment between the (conceptually translated) genomic segment and the query sequence within the ranges plus the splice (or initiation or termination) signal strengths at the both ends of the implied exon. Roughly speaking, the score is log likely ratio between observed and random probabilities, and so in general positive. However, the score depends on the sequence similarity between the genomic segment and the query sequences, which in turn depends on the evolutionary distance between them and the quality of the genomic sequence. I am afraid that I have no good idea to evaluate a proper threshold value in general cases.

Osamu

[b524198065]

Thanks a lot. Are there any filter criteria that could be conducted?

[ogotoh]

Dear Hongbo,

Spaln itself has not a filtering facility, but the associated program sortgrcd has several options to filtrate suspicious outputs. Please see the manual as for sortgrcd.

Osamu,

---

差出人: Hongbo Li [email protected] 送信日時: 2019年4月16日 11:55 宛先: ogotoh/spaln CC: 後藤修; Comment 件名: Re: [ogotoh/spaln] Question about the 6th column of spaln gff3 output (#13)

Thanks a lot. Are there any filter criteria that could be conducted?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ogotoh/spaln/issues/13#issuecomment-483491667, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AfwuLi1s_E4C0EjT6zvZF5_OL3Ni7Cyyks5vhTuvgaJpZM4bmxdP.