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nedaz / kraken

A universal genomic coordinate translator for comparative genomics
GNU General Public License v3.0
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GTF output with negative start coordinates #2

Open Victaphanta opened 7 years ago

Victaphanta commented 7 years ago

Hi again, When trying to import the GTF output into IGV, I encountered many cases of negative starting position. Not sure what went wrong. The log file had plenty of the following instances

my syntax is as follows RunKraken -c /home/victaphanta/satsuma2/kraken_Pogona_1000_pmpscgc_1000.txt -s Pogona_vitticeps.male.gtf -S Pogona_1000 -T pmpscgc_1000

double checked file and all "seems" in order.

Tell me if you need more info. Hope you can help. Thanks.

nedaz commented 7 years ago

Hi, I think this might be due to the fact that your syntenic alignments are referring to places in their nominated chromosome that do not exist. If you send me a small example of the files you are working with that have this issue I can tell you more precisely what the issue is and help you in resolving it.

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: Wednesday 23 November 2016 04:19 To: nedaz/kraken kraken@noreply.github.com<mailto:kraken@noreply.github.com> Subject: [nedaz/kraken] GTF output with negative start coordinates (#2)

Hi again, When trying to import the GTF output into IGV, I encountered many cases of negative starting position. Not sure what went wrong. The log file had plenty of the following instances

my syntax is as follows RunKraken -c /home/victaphanta/satsuma2/kraken_Pogona_1000_pmpscgc_1000.txt -s Pogona_vitticeps.male.gtf -S Pogona_1000 -T pmpscgc_1000

double checked file and all "seems" in order.

Tell me if you need more info. Hope you can help. Thanks.

— 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/2, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFLJ3MBIVMiEfr3In1b6A_C5Baya7RPlks5rA6K2gaJpZM4K6KHz.

Victaphanta commented 7 years ago

Excellent- thank you. Would you be OK if I just send you a link to the working folder. I will just place those file necessary for the current run. A

From: nedaz [mailto:notifications@github.com] Sent: Wednesday, 23 November 2016 8:14 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 output with negative start coordinates (#2)

Hi, I think this might be due to the fact that your syntenic alignments are referring to places in their nominated chromosome that do not exist. If you send me a small example of the files you are working with that have this issue I can tell you more precisely what the issue is and help you in resolving it.

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: Wednesday 23 November 2016 04:19 To: nedaz/kraken kraken@noreply.github.com<mailto:kraken@noreply.github.com> Subject: [nedaz/kraken] GTF output with negative start coordinates (#2)

Hi again, When trying to import the GTF output into IGV, I encountered many cases of negative starting position. Not sure what went wrong. The log file had plenty of the following instances

my syntax is as follows RunKraken -c /home/victaphanta/satsuma2/kraken_Pogona_1000_pmpscgc_1000.txt -s Pogona_vitticeps.male.gtf -S Pogona_1000 -T pmpscgc_1000

double checked file and all "seems" in order.

Tell me if you need more info. Hope you can help. Thanks.

— 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/2, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFLJ3MBIVMiEfr3In1b6A_C5Baya7RPlks5rA6K2gaJpZM4K6KHz.

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This e-mail is solely for the named addressee and may be confidential. You should only read, disclose, transmit, copy, distribute, act in reliance on or commercialise the contents if you are authorised to do so. If you are not the intended recipient of this e-mail, please notify postmaster@museum.vic.gov.au mailto:postmaster@museum.vic.gov.au by email immediately, or notify the sender and then destroy any copy of this message. Views expressed in this email are those of the individual sender, except where specifically stated to be those of an officer of Museum Victoria. Museum Victoria does not represent, warrant or guarantee that the integrity of this communication has been maintained nor that it is free from errors, virus or interference.

nedaz commented 7 years ago

Yes a link to the location with public access is fine.

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: Wednesday 23 November 2016 11:22 To: nedaz/kraken kraken@noreply.github.com<mailto:kraken@noreply.github.com> Cc: Neda Zamani neda.zamani@imbim.uu.se<mailto:neda.zamani@imbim.uu.se>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [nedaz/kraken] GTF output with negative start coordinates (#2)

Excellent- thank you. Would you be OK if I just send you a link to the working folder. I will just place those file necessary for the current run. A

From: nedaz [mailto:notifications@github.com] Sent: Wednesday, 23 November 2016 8:14 PM To: nedaz/kraken kraken@noreply.github.com<mailto:kraken@noreply.github.com> Cc: Moussalli, Adnan amoussalli@museum.vic.gov.au<mailto:amoussalli@museum.vic.gov.au>; Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [nedaz/kraken] GTF output with negative start coordinates (#2)

Hi, I think this might be due to the fact that your syntenic alignments are referring to places in their nominated chromosome that do not exist. If you send me a small example of the files you are working with that have this issue I can tell you more precisely what the issue is and help you in resolving it.

Best, Neda

From: Victaphanta notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> Reply-To: nedaz/kraken reply@reply.github.com<mailto:reply@reply.github.commailto:reply@reply.github.com> Date: Wednesday 23 November 2016 04:19 To: nedaz/kraken kraken@noreply.github.com<mailto:kraken@noreply.github.commailto:kraken@noreply.github.com> Subject: [nedaz/kraken] GTF output with negative start coordinates (#2)

Hi again, When trying to import the GTF output into IGV, I encountered many cases of negative starting position. Not sure what went wrong. The log file had plenty of the following instances

my syntax is as follows RunKraken -c /home/victaphanta/satsuma2/kraken_Pogona_1000_pmpscgc_1000.txt -s Pogona_vitticeps.male.gtf -S Pogona_1000 -T pmpscgc_1000

double checked file and all "seems" in order.

Tell me if you need more info. Hope you can help. Thanks.

— 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/2, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFLJ3MBIVMiEfr3In1b6A_C5Baya7RPlks5rA6K2gaJpZM4K6KHz.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nedaz/kraken/issues/2#issuecomment-262463934, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ANgWlxhaCpjNMERcsI99ULibOlMueQKSks5rBAO8gaJpZM4K6KHz.

This e-mail is solely for the named addressee and may be confidential. You should only read, disclose, transmit, copy, distribute, act in reliance on or commercialise the contents if you are authorised to do so. If you are not the intended recipient of this e-mail, please notify postmaster@museum.vic.gov.aumailto:postmaster@museum.vic.gov.au mailto:postmaster@museum.vic.gov.au by email immediately, or notify the sender and then destroy any copy of this message. Views expressed in this email are those of the individual sender, except where specifically stated to be those of an officer of Museum Victoria. Museum Victoria does not represent, warrant or guarantee that the integrity of this communication has been maintained nor that it is free from errors, virus or interference.

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Victaphanta commented 7 years ago

Here is the link

https://www.dropbox.com/sh/l9soxbqizi1jhx3/AAD6OP7n9GIqPlytaX-aqYRka?dl=0

contains the two draft genomes, the config, original GTF (and GFF) and the synteny file (actual the first step from chromosembbler).

and here is the syntax I used last:

RunKraken -c kraken_Pogona_1000_pmpscgc_1000.txt -s Pogona_vitticeps.male.gtf -S Pogona_1000 -T pmpscgc_1000 -O compare.txt -l kraken2.log -m 1000000.

Many thanks. Tell us if there is anything you need.

Adnan

From: nedaz [mailto:notifications@github.com] Sent: Wednesday, 23 November 2016 8:14 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 output with negative start coordinates (#2)

Hi, I think this might be due to the fact that your syntenic alignments are referring to places in their nominated chromosome that do not exist. If you send me a small example of the files you are working with that have this issue I can tell you more precisely what the issue is and help you in resolving it.

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: Wednesday 23 November 2016 04:19 To: nedaz/kraken kraken@noreply.github.com<mailto:kraken@noreply.github.com> Subject: [nedaz/kraken] GTF output with negative start coordinates (#2)

Hi again, When trying to import the GTF output into IGV, I encountered many cases of negative starting position. Not sure what went wrong. The log file had plenty of the following instances

my syntax is as follows RunKraken -c /home/victaphanta/satsuma2/kraken_Pogona_1000_pmpscgc_1000.txt -s Pogona_vitticeps.male.gtf -S Pogona_1000 -T pmpscgc_1000

double checked file and all "seems" in order.

Tell me if you need more info. Hope you can help. Thanks.

— 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/2, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFLJ3MBIVMiEfr3In1b6A_C5Baya7RPlks5rA6K2gaJpZM4K6KHz.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nedaz/kraken/issues/2#issuecomment-262463934, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ANgWlxhaCpjNMERcsI99ULibOlMueQKSks5rBAO8gaJpZM4K6KHz.

This e-mail is solely for the named addressee and may be confidential. You should only read, disclose, transmit, copy, distribute, act in reliance on or commercialise the contents if you are authorised to do so. If you are not the intended recipient of this e-mail, please notify postmaster@museum.vic.gov.au mailto:postmaster@museum.vic.gov.au by email immediately, or notify the sender and then destroy any copy of this message. Views expressed in this email are those of the individual sender, except where specifically stated to be those of an officer of Museum Victoria. Museum Victoria does not represent, warrant or guarantee that the integrity of this communication has been maintained nor that it is free from errors, virus or interference.