Iso-seq mapping and annotation

Question

[Ric]

Hello, We have 2 Iso-seq libaryries:

> ls -hlal 1_A01/
total 594K
drwxrws--- 2 330616 _Team 4.0K Jan 10  2018 .
drwxrws--- 4 330616 _Team 4.0K May 24  2018 ..
-rwxrwx--- 1 330616 _Team   60 Dec  4  2017 m54105_171201_020331.adapters.fasta
-rwxrwx--- 1 330616 _Team 259K Dec  4  2017 m54105_171201_020331.baz2bam_1.log
-rwxrwx--- 1 330616 _Team  14K Dec  4  2017 .m54105_171201_020331.metadata.xml
-rwxrwx--- 1 330616 _Team  51K Dec  4  2017 .m54105_171201_020331.run.metadata.xml
-rwxrwx--- 1 330616 _Team  23G Dec  4  2017 m54105_171201_020331.scraps.bam
-rwxrwx--- 1 330616 _Team  30M Dec  4  2017 m54105_171201_020331.scraps.bam.pbi
-rwxrwx--- 1 330616 _Team 105K Dec  4  2017 m54105_171201_020331.sts.xml
-rwxrwx--- 1 330616 _Team 7.9G Dec  4  2017 m54105_171201_020331.subreads.bam
-rwxrwx--- 1 330616 _Team   16 Jan 10  2018 m54105_171201_020331.subreads.bam.bai
-rwxrwx--- 1 330616 _Team  21M Dec  4  2017 m54105_171201_020331.subreads.bam.pbi
-rwxrwx--- 1 330616 _Team  16K Dec  4  2017 m54105_171201_020331.subreadset.xml
-rwxrwx--- 1 330616 _Team  535 Dec  4  2017 m54105_171201_020331.transferdone
-rwxrwx--- 1 330616 _Team 117K Dec  4  2017 tmp-file-7db72207-6fb3-415d-bfc1-34023b7b6837.txt

> ls -hlal 2_B01/
total 598K
drwxrws--- 2 330616 _Team 4.0K Dec  4  2017 .
drwxrws--- 4 330616 _Team 4.0K May 24  2018 ..
-rwxrwx--- 1 330616 _Team   60 Dec  4  2017 m54105_171201_121745.adapters.fasta
-rwxrwx--- 1 330616 _Team 268K Dec  4  2017 m54105_171201_121745.baz2bam_1.log
-rwxrwx--- 1 330616 _Team  14K Dec  4  2017 .m54105_171201_121745.metadata.xml
-rwxrwx--- 1 330616 _Team  51K Dec  4  2017 .m54105_171201_121745.run.metadata.xml
-rwxrwx--- 1 330616 _Team  23G Dec  4  2017 m54105_171201_121745.scraps.bam
-rwxrwx--- 1 330616 _Team  37M Dec  4  2017 m54105_171201_121745.scraps.bam.pbi
-rwxrwx--- 1 330616 _Team 105K Dec  4  2017 m54105_171201_121745.sts.xml
-rwxrwx--- 1 330616 _Team  11G Dec  4  2017 m54105_171201_121745.subreads.bam
-rwxrwx--- 1 330616 _Team  28M Dec  4  2017 m54105_171201_121745.subreads.bam.pbi
-rwxrwx--- 1 330616 _Team  16K Dec  4  2017 m54105_171201_121745.subreadset.xml
-rwxrwx--- 1 330616 _Team  535 Dec  4  2017 m54105_171201_121745.transferdone
-rwxrwx--- 1 330616 _Team 117K Dec  4  2017 tmp-file-990e0835-a96d-4bf3-a641-0cf498e7f112.txt

1. How can I map the Iso-seq data against our genome?
2. How can use the iso-seq data for gene prediction?

Thank you in advance,

[liorglic]

Have you tried googling this before asking? If so, what are the options you are considering?

Answer 1

[William Rowell]

There are several steps between your raw subreads (above) and aligned isoforms.

There are instructions for the most recent iso-seq analysis workflow, including CCS generation, here. If you run into any issues, please email [e-mail].