process_result Job

Biotechvana

Hola, Carlos, Bea.

YA hice todo el proceso como hablamos: la base de datos de los transcriptomas
ensamblados con Cufflinks, formateada para blast y el query con las isoformas
del gen de nuestro interés

En el último paso de Process Blast output me da este error (¿¿es error de
permisos??)

Si no fuera exactamente eso y necesitáis los ficheros xml o lo que sea decidme
por favor (o si preferis acceder al servidor, están dentro de la carpeta
hola_rick/MJB_MAPT

Ya me decìs

¡Gracias!!

Attachments

process_result_log

Biotechvana

Hola Ricardo,

Si que parece un problema de permisos.

Ahmed, could you take a look to this?

Bea

Biotechvana

Hola Ricardo,

I fixed the problem, and restarted your job again, Please check the result and
let me know if everything is ok.

Best regards,

Ahmed

Biotechvana

Thanks, Ahmed. Seems that it has finished OK. I will run the rest of the
samples and let you know.

I understand that the number of identifications is labelled in the the table
un the column “positives” right?

Thanks again

Ricardo

Biotechvana

DearAhmed. It has already finished successfully. I see some differences
between samples, which sounds great.

However, I am not sure of one question. In the column “positives” that I
interpret as the number of times this specific sequence has been found, I
always find a number of 32 (or blank in many samples and many isoforms) or a
number around 1000 in others. So it seems to me that the program is imputing a
value instead of counting . Am I right? So, the results will only say if the
isoform has been found positively or not, without quantitation?

Thanks for your help

Ricardo

Biotechvana

Hi Ricardo,

the positives column is not a quantification measure. It reports "Number
of residues that are identical or have similar chemical properties between the
query and subject sequences’ ', it is used for similarity and score
calculation in blast result.

Ahmed

Biotechvana

OK, Thanks, I see. And then, is there a quantitative measurement associated to
this test, or it is just detected / not detected?

Would there be a place where I can check the meaning of the different columns
(so I can check myself without having to ask you?)

Thanks again

ricardo

Biotechvana

Lo que vale es el evalue Ricardo. Creete unos evalues muy bajos (cuanto mas
mejor) y que tenga un hsp hit y un hsp query tambien de 50 en adelante.
Mandame el fichero y te subrayo las buenas para que veas el ejemplo

Biotechvana

te mando alguno, my friend

Gracias!!

Attachments