GTF format - 2nd column for source not transfering over

[Victaphanta]

Hi Neda, Firstly, thank you for Kraken, it is a great program.

I ran it last night and all seems to work fine. I have a gff, hence I need to convert this to GTF, which is fine. In your sample example set, however, the second column of the sample gtf simply has "protein_coding", and the transferred over as such. What I have in my annotation file, and from what I understand is typical usage for the second column, is "source", such as "cufflinks", "genewise" or "AUGUSTUS". However, these are not being recognised by Kraken. Is it possible to have any source detailed in the second column transferred to the new GTF. Thank you in advance. Adnan

[nedaz]

Hi Adnan,

If I understand you correctly, Kraken should output anything that is in the 2nd column as is with now changes. For example if you change the values of “protein_coding” to any other string in the samples it will output the transferred coordinates with that string in the second column. Can you send me an example of the transfer you made where the second column isn’t being outputted.

Best, Neda

From: Victaphanta notifications@github.com<mailto:notifications@github.com> Reply-To: nedaz/kraken reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday 22 November 2016 22:17 To: nedaz/kraken kraken@noreply.github.com<mailto:kraken@noreply.github.com> Subject: [nedaz/kraken] GTF format - 2 column for source not transfering over (#1)

Hi Neda, Firstly, thank you for Kraken, it is a great program.

I ran it last night and all seems to work fine. I have a gff, hence I need to convert this to GTF, which is fine. In your sample example set, however, the second column of the sample gtf simply has "protein_coding", and the transferred over as such. What I have in my annotation file, and from what I understand is typical usage for the second column, is "source", such as "cufflinks", "genewise" or "AUGUSTUS". However, these are not being recognised by Kraken. Is it possible to have any source detailed in the second column transferred to the new GTF. Thank you in advance. Adnan

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[Victaphanta]

Hi Neda, I ran it a second time but before doing so I modified it so that it was consistent with GTF format, rather than GFF. Specifically, and the only things that I did was to replace with gene_id “XXXX” and transcript_id “XXXX”. And it worked, Maybe there is a link somewhere there in the code that if it does not find either of these it will not obtain the source info?. Anyway – works fine now. Thank you so much for getting back to me. I also remember there being some documentation for Kraken, but it is no longer there anymore and I did not keep a copy.

Still having problems though with the negative starting coordinate.

A

From: nedaz [mailto:notifications@github.com] Sent: Wednesday, 23 November 2016 8:11 PM To: nedaz/kraken kraken@noreply.github.com Cc: Moussalli, Adnan amoussalli@museum.vic.gov.au; Author author@noreply.github.com Subject: Re: [nedaz/kraken] GTF format - 2nd column for source not transfering over (#1)

Hi Adnan,

If I understand you correctly, Kraken should output anything that is in the 2nd column as is with now changes. For example if you change the values of “protein_coding” to any other string in the samples it will output the transferred coordinates with that string in the second column. Can you send me an example of the transfer you made where the second column isn’t being outputted.

Best, Neda

From: Victaphanta notifications@github.com<mailto:notifications@github.com> Reply-To: nedaz/kraken reply@reply.github.com<mailto:reply@reply.github.com> Date: Tuesday 22 November 2016 22:17 To: nedaz/kraken kraken@noreply.github.com<mailto:kraken@noreply.github.com> Subject: [nedaz/kraken] GTF format - 2 column for source not transfering over (#1)

Hi Neda, Firstly, thank you for Kraken, it is a great program.

I ran it last night and all seems to work fine. I have a gff, hence I need to convert this to GTF, which is fine. In your sample example set, however, the second column of the sample gtf simply has "protein_coding", and the transferred over as such. What I have in my annotation file, and from what I understand is typical usage for the second column, is "source", such as "cufflinks", "genewise" or "AUGUSTUS". However, these are not being recognised by Kraken. Is it possible to have any source detailed in the second column transferred to the new GTF. Thank you in advance. Adnan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/nedaz/kraken/issues/1, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFLJ3BEDEnkPbgi4H9Dd_L0fxHm3Kg1Xks5rA03jgaJpZM4K55RP.

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